Ami Bhatt

All Publications

• Intragenic DNA inversions expand bacterial coding capacity. Nature Chanin, R. B., West, P. T., Wirbel, J., Gill, M. O., Green, G. Z., Park, R. M., Enright, N., Miklos, A. M., Hickey, A. S., Brooks, E. F., Lum, K. K., Cristea, I. M., Bhatt, A. S. 2024

  Abstract

  Bacterial populations that originate from a single bacterium are not strictly clonal and often contain subgroups with distinct phenotypes1. Bacteria can generate heterogeneity through phase variation-a preprogrammed, reversible mechanism that alters gene expression levels across a population1. One well-studied type of phase variation involves enzyme-mediated inversion of specific regions of genomic DNA2. Frequently, these DNA inversions flip the orientation of promoters, turning transcription of adjacent coding regions on or off2. Through this mechanism, inversion can affect fitness, survival or group dynamics3,4. Here, we describe the development of PhaVa, a computational tool that identifies DNA inversions using long-read datasets. We also identify 372 'intragenic invertons', a novel class of DNA inversions found entirely within genes, in genomes of bacterial and archaeal isolates. Intragenic invertons allow a gene to encode two or more versions of a protein by flipping a DNA sequence within the coding region, thereby increasing coding capacity without increasing genome size. We validate ten intragenic invertons in the gut commensal Bacteroides thetaiotaomicron, and experimentally characterize an intragenic inverton in the thiamine biosynthesis gene thiC.

  View details for DOI 10.1038/s41586-024-07970-4

  View details for PubMedID 39322669

  View details for PubMedCentralID 452554

• Phage-inclusive profiling of human gut microbiomes with Phanta. Nature biotechnology Pinto, Y., Chakraborty, M., Jain, N., Bhatt, A. S. 2023

  Abstract

  Due to technical limitations, most gut microbiome studies have focused on prokaryotes, overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the limitations of assembly-based viral profiling methods by using customized k-mer-based classification tools and incorporating recently published catalogs of gut viral genomes. Phanta's optimizations consider the small genome size of viruses, sequence homology with prokaryotes and interactions with other gut microbes. Extensive testing of Phanta on simulated data demonstrates that it quickly and accurately quantifies prokaryotes and viruses. When applied to 245 fecal metagenomes from healthy adults, Phanta identifies ~200 viral species per sample, ~5× more than standard assembly-based methods. We observe a ~2:1 ratio between DNA viruses and bacteria, with higher interindividual variability of the gut virome compared to the gut bacteriome. In another cohort, we observe that Phanta performs equally well on bulk versus virus-enriched metagenomes, making it possible to study prokaryotes and viruses in a single experiment, with a single analysis.

  View details for DOI 10.1038/s41587-023-01799-4

  View details for PubMedID 37231259

  View details for PubMedCentralID 4290017

• Quantifying bias introduced by sample collection in relative and absolute microbiome measurements. Nature biotechnology Maghini, D. G., Dvorak, M., Dahlen, A., Roos, M., Kuersten, S., Bhatt, A. S. 2023

  Abstract

  To gain insight into the accuracy of microbial measurements, it is important to evaluate sources of bias related to sample condition, preservative method and bioinformatic analyses. There is increasing evidence that measurement of the total count and concentration of microbes in the gut, or 'absolute abundance', provides a richer source of information than relative abundance and can correct some conclusions drawn from relative abundance data. However, little is known about how preservative choice can affect these measurements. In this study, we investigated how two common preservatives and short-term storage conditions impact relative and absolute microbial measurements. OMNIgene GUT OMR-200 yields lower metagenomic taxonomic variation between different storage temperatures, whereas Zymo DNA/RNA Shield yields lower metatranscriptomic taxonomic variation. Absolute abundance quantification reveals two different causes of variable Bacteroidetes:Firmicutes ratios across preservatives. Based on these results, we recommend OMNIgene GUT OMR-200 preservative for field studies and Zymo DNA/RNA Shield for metatranscriptomics studies, and we strongly encourage absolute quantification for microbial measurements.

  View details for DOI 10.1038/s41587-023-01754-3

  View details for PubMedID 37106038

  View details for PubMedCentralID 5069758

• Antimicrobial exposure is associated with decreased survival in triple-negative breast cancer. Nature communications Ransohoff, J. D., Ritter, V., Purington, N., Andrade, K., Han, S., Liu, M., Liang, S. Y., John, E. M., Gomez, S. L., Telli, M. L., Schapira, L., Itakura, H., Sledge, G. W., Bhatt, A. S., Kurian, A. W. 2023; 14 (1): 2053

  Abstract

  Antimicrobial exposure during curative-intent treatment of triple-negative breast cancer (TNBC) may lead to gut microbiome dysbiosis, decreased circulating and tumor-infiltrating lymphocytes, and inferior outcomes. Here, we investigate the association of antimicrobial exposure and peripheral lymphocyte count during TNBC treatment with survival, using integrated electronic medical record and California Cancer Registry data in the Oncoshare database. Of 772 women with stage I-III TNBC treated with and without standard cytotoxic chemotherapy - prior to the immune checkpoint inhibitor era - most (654, 85%) used antimicrobials. Applying multivariate analyses, we show that each additional total or unique monthly antimicrobial prescription is associated with inferior overall and breast cancer-specific survival. This antimicrobial-mortality association is independent of changes in neutrophil count, is unrelated to disease severity, and is sustained through year three following diagnosis, suggesting antimicrobial exposure negatively impacts TNBC survival. These results may inform mechanistic studies and antimicrobial prescribing decisions in TNBC and other hormone receptor-independent cancers.

  View details for DOI 10.1038/s41467-023-37636-0

  View details for PubMedID 37045824

  View details for PubMedCentralID 5625777

• Intragenic DNA inversions expand bacterial coding capacity. bioRxiv : the preprint server for biology Chanin, R. B., West, P. T., Park, R. M., Wirbel, J., Green, G. Z., Miklos, A. M., Gill, M. O., Hickey, A. S., Brooks, E. F., Bhatt, A. S. 2023

  Abstract

  Bacterial populations that originate from a single bacterium are not strictly clonal. Often they contain subgroups that have distinct phenotypes. One way that bacteria generate this heterogeneity is through phase variation: enzyme-mediated, reversible inversion of specific intergenic regions of genomic DNA. These DNA inversions can flip the orientation of promoters within otherwise isogenic populations, impacting fitness and survival. We developed and applied bioinformatic approaches that enabled the discovery of thousands of previously undescribed phase-variable regions in prokaryotes using long-read datasets. We identified 'intragenic invertons', a surprising new class of invertible elements found entirely within genes, across the prokaryotic tree of life. Intragenic invertons allow a single gene to encode two or more versions of a protein by flipping a DNA sequence within the gene, thereby increasing coding capacity without increasing genome size. We experimentally characterize specific intragenic invertons in the gut commensal Bacteroides thetaiotaomicron , presenting a 'roadmap' for investigating this gene-diversifying phenomenon.One-Sentence Summary: Intragenic DNA inversions, identified using long-read sequencing datasets, are found across the prokaryotic tree of life.

  View details for DOI 10.1101/2023.03.11.532203

  View details for PubMedID 36945655

• Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome. Nature biotechnology Durrant, M. G., Fanton, A., Tycko, J., Hinks, M., Chandrasekaran, S. S., Perry, N. T., Schaepe, J., Du, P. P., Lotfy, P., Bassik, M. C., Bintu, L., Bhatt, A. S., Hsu, P. D. 2022

  Abstract

  Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as Bxb1 and PhiC31, have been characterized to date, with limited efficiency as tools for DNA integration in human cells. In this study, we developed a computational approach to identify thousands of LSRs and their DNA attachment sites, expanding known LSR diversity by >100-fold and enabling the prediction of their insertion site specificities. We tested their recombination activity in human cells, classifying them as landing pad, genome-targeting or multi-targeting LSRs. Overall, we achieved up to seven-fold higher recombination than Bxb1 and genome integration efficiencies of 40-75% with cargo sizes over 7kb. We also demonstrate virus-free, direct integration of plasmid or amplicon libraries for improved functional genomics applications. This systematic discovery of recombinases directly from microbial sequencing data provides a resource of over 60 LSRs experimentally characterized in human cells for large-payload genome insertion without exposed DNA double-stranded breaks.

  View details for DOI 10.1038/s41587-022-01494-w

  View details for PubMedID 36217031

• Equitable partnerships and the path to inclusive, innovative and impactful human microbiome research. Nature reviews. Gastroenterology & hepatology Oduaran, O. H., Bhatt, A. S. 2022

  View details for DOI 10.1038/s41575-022-00689-5

  View details for PubMedID 36171273

• Complete, closed bacterial genomes from microbiomes using nanopore sequencing. Nature biotechnology Moss, E. L., Maghini, D. G., Bhatt, A. S. 2020

  Abstract

  Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements. Correct assignment of genomic positions of repeats is crucial for understanding the effect of genome structure on genome function. We applied nanopore sequencing and our workflow, named Lathe, which incorporates long-read assembly and short-read error correction, to assemble closed bacterial genomes from complex microbiomes. We validated our approach with a synthetic mixture of 12 bacterial species. Seven genomes were completely assembled into single contigs and three genomes were assembled into four or fewer contigs. Next, we used our methods to analyze metagenomics data from 13 human stool samples. We assembled 20 circular genomes, including genomes of Prevotella copri and a candidate Cibiobacter sp. Despite the decreased nucleotide accuracy compared with alternative sequencing and assembly approaches, our methods improved assembly contiguity, allowing for investigation of the role of repeat elements in microbial function and adaptation.

  View details for DOI 10.1038/s41587-020-0422-6

  View details for PubMedID 32042169

• Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes. Cell Sberro, H., Fremin, B. J., Zlitni, S., Edfors, F., Greenfield, N., Snyder, M. P., Pavlopoulos, G. A., Kyrpides, N. C., Bhatt, A. S. 2019

  Abstract

  Small proteins are traditionally overlooked due to computational and experimental difficulties in detecting them. To systematically identify small proteins, we carried out a comparative genomics study on 1,773 human-associated metagenomes from four different body sites. We describe >4,000 conserved protein families, the majority of which are novel; 30% of these protein families are predicted to be secreted or transmembrane. Over 90% of the small protein families have no known domain and almost half are not represented in reference genomes. We identify putative housekeeping, mammalian-specific, defense-related, and protein families that are likely to be horizontally transferred. We provide evidence of transcription and translation for a subset of these families. Our study suggests that small proteins are highly abundant and those of the human microbiome, in particular, may perform diverse functions that have not been previously reported.

  View details for DOI 10.1016/j.cell.2019.07.016

  View details for PubMedID 31402174

• Precision identification of diverse bloodstream pathogens in the gut microbiome NATURE MEDICINE Tamburini, F. B., Andermann, T. M., Tkachenko, E., Senchyna, F., Banaei, N., Bhatt, A. S. 2018; 24 (12): 1809-+

  View details for DOI 10.1038/s41591-018-0202-8

  View details for Web of Science ID 000452392200008

• Viroid-like colonists of human microbiomes. Cell Zheludev, I. N., Edgar, R. C., Lopez-Galiano, M. J., de la Peña, M., Babaian, A., Bhatt, A. S., Fire, A. Z. 2024

  Abstract

  Here, we describe "obelisks," a class of heritable RNA elements sharing several properties: (1) apparently circular RNA ∼1 kb genome assemblies, (2) predicted rod-like genome-wide secondary structures, and (3) open reading frames encoding a novel "Oblin" protein superfamily. A subset of obelisks includes a variant hammerhead self-cleaving ribozyme. Obelisks form their own phylogenetic group without detectable similarity to known biological agents. Surveying globally, we identified 29,959 distinct obelisks (clustered at 90% sequence identity) from diverse ecological niches. Obelisks are prevalent in human microbiomes, with detection in ∼7% (29/440) and ∼50% (17/32) of queried stool and oral metatranscriptomes, respectively. We establish Streptococcus sanguinis as a cellular host of a specific obelisk and find that this obelisk's maintenance is not essential for bacterial growth. Our observations identify obelisks as a class of diverse RNAs of yet-to-be-determined impact that have colonized and gone unnoticed in human and global microbiomes.

  View details for DOI 10.1016/j.cell.2024.09.033

  View details for PubMedID 39481381

• Mining human microbiomes reveals an untapped source of peptide antibiotics. Cell Torres, M. D., Brooks, E. F., Cesaro, A., Sberro, H., Gill, M. O., Nicolaou, C., Bhatt, A. S., de la Fuente-Nunez, C. 2024

  Abstract

  Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally screened 444,054 previously reported putative small protein families from 1,773 human metagenomes for antimicrobial properties, identifying 323 candidates encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro, with 70.5% displaying antimicrobial activity. As these compounds were different compared with previously reported antimicrobial peptides, we termed them smORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergizing with each other, and modulating gut commensals, indicating a potential role in reconfiguring microbiome communities in addition to counteracting pathogens. The lead candidates were anti-infective in both murine skin abscess and deep thigh infection models. Notably, prevotellin-2 from Prevotella copri presented activity comparable to the commonly used antibiotic polymyxin B. Our report supports the existence of hundreds of antimicrobials in the human microbiome amenable to clinical translation.

  View details for DOI 10.1016/j.cell.2024.07.027

  View details for PubMedID 39163860

• Differentiation of Prior SARS-CoV-2 Infection and Postacute Sequelae by Standard Clinical Laboratory Measurements in the RECOVER Cohort. Annals of internal medicine Erlandson, K. M., Geng, L. N., Selvaggi, C. A., Thaweethai, T., Chen, P., Erdmann, N. B., Goldman, J. D., Henrich, T. J., Hornig, M., Karlson, E. W., Katz, S. D., Kim, C., Cribbs, S. K., Laiyemo, A. O., Letts, R., Lin, J. Y., Marathe, J., Parthasarathy, S., Patterson, T. F., Taylor, B. D., Duffy, E. R., Haack, M., Julg, B., Maranga, G., Hernandez, C., Singer, N. G., Han, J., Pemu, P., Brim, H., Ashktorab, H., Charney, A. W., Wisnivesky, J., Lin, J. J., Chu, H. Y., Go, M., Singh, U., Levitan, E. B., Goepfert, P. A., Nikolich, J. Ž., Hsu, H., Peluso, M. J., Kelly, J. D., Okumura, M. J., Flaherman, V. J., Quigley, J. G., Krishnan, J. A., Scholand, M. B., Hess, R., Metz, T. D., Costantine, M. M., Rouse, D. J., Taylor, B. S., Goldberg, M. P., Marshall, G. D., Wood, J., Warren, D., Horwitz, L., Foulkes, A. S., McComsey, G. A. 2024

  Abstract

  There are currently no validated clinical biomarkers of postacute sequelae of SARS-CoV-2 infection (PASC).To investigate clinical laboratory markers of SARS-CoV-2 and PASC.Propensity score-weighted linear regression models were fitted to evaluate differences in mean laboratory measures by prior infection and PASC index (≥12 vs. 0). (ClinicalTrials.gov: NCT05172024).83 enrolling sites.RECOVER-Adult cohort participants with or without SARS-CoV-2 infection with a study visit and laboratory measures 6 months after the index date (or at enrollment if >6 months after the index date). Participants were excluded if the 6-month visit occurred within 30 days of reinfection.Participants completed questionnaires and standard clinical laboratory tests.Among 10 094 participants, 8746 had prior SARS-CoV-2 infection, 1348 were uninfected, 1880 had a PASC index of 12 or higher, and 3351 had a PASC index of zero. After propensity score adjustment, participants with prior infection had a lower mean platelet count (265.9 × 109 cells/L [95% CI, 264.5 to 267.4 × 109 cells/L]) than participants without known prior infection (275.2 × 109 cells/L [CI, 268.5 to 282.0 × 109 cells/L]), as well as higher mean hemoglobin A1c (HbA1c) level (5.58% [CI, 5.56% to 5.60%] vs. 5.46% [CI, 5.40% to 5.51%]) and urinary albumin-creatinine ratio (81.9 mg/g [CI, 67.5 to 96.2 mg/g] vs. 43.0 mg/g [CI, 25.4 to 60.6 mg/g]), although differences were of modest clinical significance. The difference in HbA1c levels was attenuated after participants with preexisting diabetes were excluded. Among participants with prior infection, no meaningful differences in mean laboratory values were found between those with a PASC index of 12 or higher and those with a PASC index of zero.Whether differences in laboratory markers represent consequences of or risk factors for SARS-CoV-2 infection could not be determined.Overall, no evidence was found that any of the 25 routine clinical laboratory values assessed in this study could serve as a clinically useful biomarker of PASC.National Institutes of Health.

  View details for DOI 10.7326/M24-0737

  View details for PubMedID 39133923

• Dual quorum-sensing control of purine biosynthesis drives pathogenic fitness of Enterococcus faecalis. bioRxiv : the preprint server for biology Zlitni, S., Bowden, S., Sberro, H., Torres, M. D., Vaughan, J. M., Pinto, A. F., Pinto, Y., Fernandez, D., Röst, H., Saghatelian, A., de la Fuente-Nunez, C., Bhatt, A. S. 2024

  Abstract

  Enterococcus faecalis is a resident of the human gut, though upon translocation to the blood or body tissues, it can be pathogenic. Here we discover and characterize two peptide-based quorum-sensing systems that transcriptionally modulate de novo purine biosynthesis in E. faecalis. Using a comparative genomic analysis, we find that most enterococcal species do not encode this system; E. moraviensis, E. haemoperoxidus and E. caccae, three species that are closely related to E. faecalis, encode one of the two systems, and only E. faecalis encodes both systems. We show that these systems are important for the intracellular survival of E. faecalis within macrophages and for the fitness of E. faecalis in a murine wound infection model. Taken together, we combine comparative genomics, microbiological, bacterial genetics, transcriptomics, targeted proteomics and animal model experiments to describe a paired quorum sensing mechanism that directly influences central metabolism and impacts the pathogenicity of E. faecalis.

  View details for DOI 10.1101/2024.08.13.607696

  View details for PubMedID 39185165

  View details for PubMedCentralID PMC11343167

• Sequencing-based analysis of microbiomes. Nature reviews. Genetics Pinto, Y., Bhatt, A. S. 2024

  Abstract

  Microbiomes occupy a range of niches and, in addition to having diverse compositions, they have varied functional roles that have an impact on agriculture, environmental sciences, and human health and disease. The study of microbiomes has been facilitated by recent technological and analytical advances, such as cheaper and higher-throughput DNA and RNA sequencing, improved long-read sequencing and innovative computational analysis methods. These advances are providing a deeper understanding of microbiomes at the genomic, transcriptional and translational level, generating insights into their function and composition at resolutions beyond the species level.

  View details for DOI 10.1038/s41576-024-00746-6

  View details for PubMedID 38918544

  View details for PubMedCentralID 9034083

• Temperature-dependent differences in mouse gut motility are mediated by stress. Lab animal Han, A., Hudson-Paz, C., Robinson, B. G., Becker, L., Jacobson, A., Kaltschmidt, J. A., Garrison, J. L., Bhatt, A. S., Monack, D. M. 2024

  Abstract

  Researchers have advocated elevating mouse housing temperatures from the conventional ~22 °C to the mouse thermoneutral point of 30 °C to enhance translational research. However, the impact of environmental temperature on mouse gastrointestinal physiology remains largely unexplored. Here we show that mice raised at 22 °C exhibit whole gut transit speed nearly twice as fast as those raised at 30 °C, primarily driven by a threefold increase in colon transit speed. Furthermore, gut microbiota composition differs between the two temperatures but does not dictate temperature-dependent differences in gut motility. Notably, increased stress signals from the hypothalamic-pituitary-adrenal axis at 22 °C have a pivotal role in mediating temperature-dependent differences in gut motility. Pharmacological and genetic depletion of the stress hormone corticotropin-releasing hormone slows gut motility in stressed 22 °C mice but has no comparable effect in relatively unstressed 30 °C mice. In conclusion, our findings highlight that colder mouse facility temperatures significantly increase gut motility through hormonal stress pathways.

  View details for DOI 10.1038/s41684-024-01376-5

  View details for PubMedID 38806681

  View details for PubMedCentralID 3371737

• Envisioning Academic Global Oncologists: Proposed Competencies for Global Oncology Training From ASCO. JCO global oncology Bourlon, M. T., Bhatt, A. S., Lopes, G., Asirwa, F. C., Eniu, A. E., Loehrer, P. J., Shulman, L. N., Close, J., Von Roenn, J., Tibbits, M., Pyle, D., Gralow, J. R. 2024; 10: e2300157

  Abstract

  Recognizing the rising incidence, prevalence, and mortality of cancer in low- and middle-resource settings, as well as the increasingly international profile of its membership, ASCO has committed to expanding its engagement at a global level. In 2017, the ASCO Academic Global Oncology Task Force sought to define the potential role for ASCO in supporting global oncology as an academic field. A set of recommendations to advance the status of global oncology as an academic discipline were created through a consensus-based process involving participation by a diverse group of global oncology and global health practitioners; these recommendations were then published. The recommendations included developing a set of global oncology competencies for trainees and faculty interested in a career in academic global oncology. Here, we describe the global oncology competencies developed by this task force. These competencies consist of knowledge and skills needed in general global health as well as cancer-specific care and research, including understanding global cancer health disparities, defining unique resources and needs in low- and middle-resource settings, and promoting international collaboration. Although the competencies were originally developed for US training programs, they are intended to be widely applicable globally. By formalizing the training of oncologists and supporting career pathways in the field of global oncology, we can make progress in achieving global equity in cancer care and control.

  View details for DOI 10.1200/GO.23.00157

  View details for PubMedID 38603655

• Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle. bioRxiv : the preprint server for biology Schmidtke, D. T., Hickey, A. S., Liachko, I., Sherlock, G., Bhatt, A. S. 2024

  Abstract

  The prototypic crAssphage ( Carjivirus communis ) is one of the most abundant, prevalent, and persistent gut bacteriophages, yet it remains uncultured and its lifestyle uncharacterized. For the last decade, crAssphage has escaped plaque-dependent culturing efforts, leading us to investigate alternative lifestyles that might explain its widespread success. Through genomic analyses and culturing, we find that crAssphage uses a phage-plasmid lifestyle to persist extrachromosomally. Plasmid-related genes are more highly expressed than those implicated in phage maintenance. Leveraging this finding, we use a plaque-free culturing approach to measure crAssphage replication in culture with Phocaeicola vulgatus, Phocaeicola dorei, and Bacteroides stercoris , revealing a broad host range. We demonstrate that crAssphage persists with its hosts in culture without causing major cell lysis events or integrating into host chromosomes. The ability to switch between phage and plasmid lifestyles within a wide range of hosts contributes to the prolific nature of crAssphage in the human gut microbiome.

  View details for DOI 10.1101/2024.03.20.585998

  View details for PubMedID 38562748

• Expanding the human gut microbiome atlas of Africa. bioRxiv : the preprint server for biology Maghini, D. G., Oduaran, O. H., Wirbel, J., Olubayo, L. A., Smyth, N., Mathema, T., Belger, C. W., Agongo, G., Boua, P. R., Choma, S. S., Gómez-Olivé, F. X., Kisiangani, I., Mashaba, G. R., Micklesfield, L., Mohamed, S. F., Nonterah, E. A., Norris, S., Sorgho, H., Tollman, S., Wafawanaka, F., Tluway, F., Ramsay, M., Bhatt, A. S., Hazelhurst, S. 2024

  Abstract

  Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ~84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the world's population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens. Finally, we find a microbiome signature of HIV infection that is defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research.

  View details for DOI 10.1101/2024.03.13.584859

  View details for PubMedID 38559015

  View details for PubMedCentralID PMC10980044

• The journey to understand previously unknown microbial genes. Nature Wirbel, J., Bhatt, A. S., Probst, A. J. 2024

  View details for DOI 10.1038/d41586-024-00077-w

  View details for PubMedID 38291331

• Viroid-like colonists of human microbiomes. bioRxiv : the preprint server for biology Zheludev, I. N., Edgar, R. C., Lopez-Galiano, M. J., de la Pena, M., Babaian, A., Bhatt, A. S., Fire, A. Z. 2024

  Abstract

  Here, we describe the "Obelisks," a previously unrecognised class of viroid-like elements that we first identified in human gut metatranscriptomic data. "Obelisks" share several properties: (i) apparently circular RNA 1kb genome assemblies, (ii) predicted rod-like secondary structures encompassing the entire genome, and (iii) open reading frames coding for a novel protein superfamily, which we call the "Oblins". We find that Obelisks form their own distinct phylogenetic group with no detectable sequence or structural similarity to known biological agents. Further, Obelisks are prevalent in tested human microbiome metatranscriptomes with representatives detected in 7% of analysed stool metatranscriptomes (29/440) and in 50% of analysed oral metatranscriptomes (17/32). Obelisk compositions appear to differ between the anatomic sites and are capable of persisting in individuals, with continued presence over >300 days observed in one case. Large scale searches identified 29,959 Obelisks (clustered at 90% nucleotide identity), with examples from all seven continents and in diverse ecological niches. From this search, a subset of Obelisks are identified to code for Obelisk-specific variants of the hammerhead type-III self-cleaving ribozyme. Lastly, we identified one case of a bacterial species ( Streptococcus sanguinis ) in which a subset of defined laboratory strains harboured a specific Obelisk RNA population. As such, Obelisks comprise a class of diverse RNAs that have colonised, and gone unnoticed in, human, and global microbiomes.

  View details for DOI 10.1101/2024.01.20.576352

  View details for PubMedID 38293115

• Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition. Cell Gerrick, E. R., Zlitni, S., West, P. T., Carter, M. M., Mechler, C. M., Olm, M. R., Caffrey, E. B., Li, J. A., Higginbottom, S. K., Severyn, C. J., Kracke, F., Spormann, A. M., Sonnenburg, J. L., Bhatt, A. S., Howitt, M. R. 2023

  Abstract

  The microbiota influences intestinal health and physiology, yet the contributions of commensal protists to the gut environment have been largely overlooked. Here, we discover human- and rodent-associated parabasalid protists, revealing substantial diversity and prevalence in nonindustrialized human populations. Genomic and metabolomic analyses of murine parabasalids from the genus Tritrichomonas revealed species-level differences in excretion of the metabolite succinate, which results in distinct small intestinal immune responses. Metabolic differences between Tritrichomonas species also determine their ecological niche within the microbiota. By manipulating dietary fibers and developing in vitro protist culture, we show that different Tritrichomonas species prefer dietary polysaccharides or mucus glycans. These polysaccharide preferences drive trans-kingdom competition with specific commensal bacteria, which affects intestinal immunity in a diet-dependent manner. Our findings reveal unappreciated diversity in commensal parabasalids, elucidate differences in commensal protist metabolism, and suggest how dietary interventions could regulate their impact on gut health.

  View details for DOI 10.1016/j.cell.2023.11.018

  View details for PubMedID 38096822

• Hybrid assemblies of microbiomeBlastocystisprotists reveal evolutionary diversification reflecting host ecology. bioRxiv : the preprint server for biology Lind, A. L., McDonald, N. A., Gerrick, E. R., Bhatt, A. S., Pollard, K. S. 2023

  Abstract

  The most prevalent microbial eukaryote in the human gut is Blastocystis , an obligate commensal protist also common in many other vertebrates. Blastocystis is descended from free-living stramenopile ancestors; how it has adapted to thrive within humans and a wide range of hosts is unclear. Here, we cultivated six Blastocystis strains spanning the diversity of the genus and generated highly contiguous, annotated genomes with long-read DNA-seq, Hi-C, and RNA-seq. Comparative genomics between these strains and two closely related stramenopiles with different lifestyles, the lizard gut symbiont Proteromonas lacertae and the free-living marine flagellate Cafeteria burkhardae , reveal the evolutionary history of the Blastocystis genus. We find substantial gene content variability between Blastocystis strains. Blastocystis isolated from an herbivorous tortoise has many plant carbohydrate metabolizing enzymes, some horizontally acquired from bacteria, likely reflecting fermentation within the host gut. In contrast, human- isolated Blastocystis have gained many heat shock proteins, and we find numerous subtype- specific expansions of host-interfacing genes, including cell adhesion and cell surface glycan genes. In addition, we observe that human-isolated Blastocystis have substantial changes in gene structure, including shortened introns and intergenic regions, as well as genes lacking canonical termination codons. Finally, our data indicate that the common ancestor of Blastocystis lost nearly all ancestral genes for heterokont flagella morphology, including cilia proteins, microtubule motor proteins, and ion channel proteins. Together, these findings underscore the huge functional variability within the Blastocystis genus and provide candidate genes for the adaptations these lineages have undergone to thrive in the gut microbiomes of diverse vertebrates.

  View details for DOI 10.1101/2023.11.20.567959

  View details for PubMedID 38045412

• Acute steroid-refractory GI GVHD is not associated with significant differences in gut taxonomic composition compared to steroid-sensitive GI GVHD immediately prior to onset of disease: GI GVHD is not characterized by gut microbial differences preceding symptom onset. Transplantation and cellular therapy Zeng, K., Brewster, R., Kang, J. B., Tkachenko, E., Brooks, E., Bhatt, A. S., Fodor, A. A., Andermann, T. M. 2023

  Abstract

  Taxonomic composition of the gut microbiota at the time of neutrophil engraftment is associated with the development of acute gastrointestinal graft-versus-host disease (GI GVHD) in patients undergoing allogeneic hematopoietic stem cell transplantation. However, less is known about the relationship between the gut microbiota and development of steroid-refractory GI GVHD immediately prior to the onset of disease.Markers of steroid-refractory GI GVHD are needed in order to identify patients who may benefit from the early initiation of non-corticosteroid-based GVHD treatment. Our aim was to identify differences in taxonomic composition in stool samples from patients without GVHD, with steroid-responsive GVHD and with steroid-refractory GI GVHD in order to identify predictive microbiome biomarkers of steroid-refractory GI GVHD.We conducted a retrospective case-control, single institution study, performing shotgun metagenomic sequencing on stool samples from patients with (n=36) and without GVHD (n=34) matched for time since transplant. We compared the taxonomic composition of the gut microbiome in those with steroid-sensitive GI GVHD (n=17) and steroid-refractory GI GVHD (n=19) to each other and to those without GVHD. We also performed associations between steroid-refractory GI GVHD, gut taxonomic composition, and fecal calprotectin, a marker of GI GVHD to develop composite fecal markers of steroid-refractory GVHD prior to the onset of GI disease.We found that fecal samples within 30 days of GVHD onset from patients with and without GVHD or with and without steroid-refractory GI GVHD did not differ significantly in Shannon diversity (alpha-diversity) or in overall taxonomic composition (beta-diversity). While those patients without GVHD had higher relative abundance of Clostridium spp., those with and without steroid-refractory GI GVHD did not significantly differ in taxonomic composition between one another. In our study, fecal calprotectin prior to disease onset was significantly higher in patients with GVHD compared to those without GVHD and higher in patients with steroid-refractory GI GVHD compared to steroid-sensitive GI GVHD. No taxa were significantly associated with higher levels of calprotectin.

  View details for DOI 10.1016/j.jtct.2023.11.006

  View details for PubMedID 37944820

• Identification of over ten thousand candidate structured RNAs in viruses and phages. Computational and structural biotechnology journal Fremin, B. J., Bhatt, A. S., Kyrpides, N. C. 2023; 21: 5630-5639

  Abstract

  Structured RNAs play crucial roles in viruses, exerting influence over both viral and host gene expression. However, the extensive diversity of structured RNAs and their ability to act in cis or trans positions pose challenges for predicting and assigning their functions. While comparative genomics approaches have successfully predicted candidate structured RNAs in microbes on a large scale, similar efforts for viruses have been lacking. In this study, we screened over 5 million DNA and RNA viral sequences, resulting in the prediction of 10,006 novel candidate structured RNAs. These predictions are widely distributed across taxonomy and ecosystem. We found transcriptional evidence for 206 of these candidate structured RNAs in the human fecal microbiome. These candidate RNAs exhibited evidence of nucleotide covariation, indicative of selective pressure maintaining the predicted secondary structures. Our analysis revealed a diverse repertoire of candidate structured RNAs, encompassing a substantial number of putative tRNAs or tRNA-like structures, Rho-independent transcription terminators, and potentially cis-regulatory structures consistently positioned upstream of genes. In summary, our findings shed light on the extensive diversity of structured RNAs in viruses, offering a valuable resource for further investigations into their functional roles and implications in viral gene expression and pave the way for a deeper understanding of the intricate interplay between viruses and their hosts at the molecular level.

  View details for DOI 10.1016/j.csbj.2023.11.010

  View details for PubMedID 38047235

  View details for PubMedCentralID PMC10690425

• Large-Scale Post-Transplant TCR Deep Sequencing Reveals a Major T Cell Diversity Bottleneck with Post-Transplant Cyclophosphamide with Implications for Both Efficacy and Toxicity: Results of the BMT CTN 1801 Study Kean, L., Siegel, S. J., Schmalz, J. T., Bien, S. A., Scheffey, D., Sanders, C., Robins, H., Applegate, K., Bar, M., Chhabra, S., Choi, S. W., Clark, W., Das, S. R., Jenq, R. R., Jones, R. J., Levine, J., Logan, B. R., Murthy, H. S., Rashidi, A., Riches, M. L., Saber, W., Sandhu, K. S., Sung, A. D., Larkin, K., Al Malki, M. M., Gooptu, M., Elmariah, H., Alousi, A., Runaas, L., Shaffer, B. C., Rezvani, A. R., El Jurdi, N., Loren, A., Horowitz, M. M., Bolanos-Meade, J., Holtan, S. G., Bhatt, A. S., Perales, M., DeWolf, S. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-188032

  View details for Web of Science ID 001159306701232

• Human gut metagenomic mining reveals an untapped source of peptide antibiotics. bioRxiv : the preprint server for biology Torres, M. D., Brooks, E., Cesaro, A., Sberro, H., Nicolaou, C., Bhatt, A. S., de la Fuente-Nunez, C. 2023

  Abstract

  Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally mined 444,054 families of putative small proteins from 1,773 human gut metagenomes, identifying 323 peptide antibiotics encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro , with 59% displaying activity against either pathogens or commensals. Since these peptides were unique compared to previously reported antimicrobial peptides, we termed them s mORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergized with each other, and modulated gut commensals, indicating that they may play a role in reconfiguring microbiome communities in addition to counteracting pathogens. The lead candidates were anti-infective in both murine skin abscess and deep thigh infection models. Notably, prevotellin-2 from Prevotella copri presented activity comparable to the commonly used antibiotic polymyxin B. We report the discovery of hundreds of peptide sequences in the human gut.

  View details for DOI 10.1101/2023.08.31.555711

  View details for PubMedID 37693399

• The Tomato Brown Rugose Fruit Virus Movement Protein Gene Is a Novel Microbial Source Tracking Marker. Applied and environmental microbiology Natarajan, A., Fremin, B. J., Schmidtke, D. T., Wolfe, M. K., Zlitni, S., Graham, K. E., Brooks, E. F., Severyn, C. J., Sakamoto, K. M., Lacayo, N. J., Kuersten, S., Koble, J., Caves, G., Kaplan, I., Singh, U., Jagannathan, P., Rezvani, A. R., Bhatt, A. S., Boehm, A. B. 2023: e0058323

  Abstract

  Microbial source tracking (MST) identifies sources of fecal contamination in the environment using host-associated fecal markers. While there are numerous bacterial MST markers that can be used herein, there are few such viral markers. Here, we designed and tested novel viral MST markers based on tomato brown rugose fruit virus (ToBRFV) genomes. We assembled eight nearly complete genomes of ToBRFV from wastewater and stool samples from the San Francisco Bay Area in the United States. Next, we developed two novel probe-based reverse transcription-PCR (RT-PCR) assays based on conserved regions of the ToBRFV genome and tested the markers' sensitivities and specificities using human and non-human animal stool as well as wastewater. The ToBRFV markers are sensitive and specific; in human stool and wastewater, they are more prevalent and abundant than a commonly used viral marker, the pepper mild mottle virus (PMMoV) coat protein (CP) gene. We used the assays to detect fecal contamination in urban stormwater samples and found that the ToBRFV markers matched cross-assembly phage (crAssphage), an established viral MST marker, in prevalence across samples. Taken together, these results indicate that ToBRFV is a promising viral human-associated MST marker. IMPORTANCE Human exposure to fecal contamination in the environment can cause transmission of infectious diseases. Microbial source tracking (MST) can identify sources of fecal contamination so that contamination can be remediated and human exposures can be reduced. MST requires the use of host-associated MST markers. Here, we designed and tested novel MST markers from genomes of tomato brown rugose fruit virus (ToBRFV). The markers are sensitive and specific to human stool and highly abundant in human stool and wastewater samples.

  View details for DOI 10.1128/aem.00583-23

  View details for PubMedID 37404180

• Post-Transplantation Cyclophosphamide-Based Graft-versus-Host Disease Prophylaxis. The New England journal of medicine Bolaños-Meade, J., Hamadani, M., Wu, J., Al Malki, M. M., Martens, M. J., Runaas, L., Elmariah, H., Rezvani, A. R., Gooptu, M., Larkin, K. T., Shaffer, B. C., El Jurdi, N., Loren, A. W., Solh, M., Hall, A. C., Alousi, A. M., Jamy, O. H., Perales, M. A., Yao, J. M., Applegate, K., Bhatt, A. S., Kean, L. S., Efebera, Y. A., Reshef, R., Clark, W., DiFronzo, N. L., Leifer, E., Horowitz, M. M., Jones, R. J., Holtan, S. G. 2023; 388 (25): 2338-2348

  Abstract

  In patients undergoing allogeneic hematopoietic stem-cell transplantation (HSCT), a calcineurin inhibitor plus methotrexate has been a standard prophylaxis against graft-versus-host disease (GVHD). A phase 2 study indicated the potential superiority of a post-transplantation regimen of cyclophosphamide, tacrolimus, and mycophenolate mofetil.In a phase 3 trial, we randomly assigned adults with hematologic cancers in a 1:1 ratio to receive cyclophosphamide-tacrolimus-mycophenolate mofetil (experimental prophylaxis) or tacrolimus-methotrexate (standard prophylaxis). The patients underwent HSCT from an HLA-matched related donor or a matched or 7/8 mismatched (i.e., mismatched at only one of the HLA-A, HLA-B, HLA-C, and HLA-DRB1 loci) unrelated donor, after reduced-intensity conditioning. The primary end point was GVHD-free, relapse-free survival at 1 year, assessed in a time-to-event analysis, with events defined as grade III or IV acute GVHD, chronic GVHD warranting systemic immunosuppression, disease relapse or progression, and death from any cause.In a multivariate Cox regression analysis, GVHD-free, relapse-free survival was significantly more common among the 214 patients in the experimental-prophylaxis group than among the 217 patients in the standard-prophylaxis group (hazard ratio for grade III or IV acute GVHD, chronic GVHD, disease relapse or progression, or death, 0.64; 95% confidence interval [CI], 0.49 to 0.83; P = 0.001). At 1 year, the adjusted GVHD-free, relapse-free survival was 52.7% (95% CI, 45.8 to 59.2) with experimental prophylaxis and 34.9% (95% CI, 28.6 to 41.3) with standard prophylaxis. Patients in the experimental-prophylaxis group appeared to have less severe acute or chronic GVHD and a higher incidence of immunosuppression-free survival at 1 year. Overall and disease-free survival, relapse, transplantation-related death, and engraftment did not differ substantially between the groups.Among patients undergoing allogeneic HLA-matched HSCT with reduced-intensity conditioning, GVHD-free, relapse-free survival at 1 year was significantly more common among those who received cyclophosphamide-tacrolimus-mycophenolate mofetil than among those who received tacrolimus-methotrexate. (Funded by the National Heart, Lung, and Blood Institute and others; BMT CTN 1703 ClinicalTrials.gov number, NCT03959241.).

  View details for DOI 10.1056/NEJMoa2215943

  View details for PubMedID 37342922

• Chemoproteomic identification of a DPP4 homolog in Bacteroides thetaiotaomicron. Nature chemical biology Keller, L. J., Nguyen, T. H., Liu, L. J., Hurysz, B. M., Lakemeyer, M., Guerra, M., Gelsinger, D. J., Chanin, R., Ngo, N., Lum, K. M., Faucher, F., Ipock, P., Niphakis, M. J., Bhatt, A. S., O'Donoghue, A. J., Huang, K. C., Bogyo, M. 2023

  Abstract

  Serine hydrolases have important roles in signaling and human metabolism, yet little is known about their functions in gut commensal bacteria. Using bioinformatics and chemoproteomics, we identify serine hydrolases in the gut commensal Bacteroides thetaiotaomicron that are specific to the Bacteroidetes phylum. Two are predicted homologs of the human dipeptidyl peptidase 4 (hDPP4), a key enzyme that regulates insulin signaling. Our functional studies reveal that BT4193 is a true homolog of hDPP4 that can be inhibited by FDA-approved type 2 diabetes medications targeting hDPP4, while the other is a misannotated proline-specific triaminopeptidase. We demonstrate that BT4193 is important for envelope integrity and that loss of BT4193 reduces B. thetaiotaomicron fitness during in vitro growth within a diverse community. However, neither function is dependent on BT4193 proteolytic activity, suggesting a scaffolding or signaling function for this bacterial protease.

  View details for DOI 10.1038/s41589-023-01357-8

  View details for PubMedID 37349583

  View details for PubMedCentralID 6108420

• Phage diversity in cell-free DNA identifies bacterial pathogens in human sepsis cases. Nature microbiology Haddock, N. L., Barkal, L. J., Ram-Mohan, N., Kaber, G., Chiu, C. Y., Bhatt, A. S., Yang, S., Bollyky, P. L. 2023

  Abstract

  Bacteriophages, viruses that infect bacteria, have great specificity for their bacterial hosts at the strain and species level. However, the relationship between the phageome and associated bacterial population dynamics is unclear. Here we generated a computational pipeline to identify sequences associated with bacteriophages and their bacterial hosts in cell-free DNA from plasma samples. Analysis of two independent cohorts, including a Stanford Cohort of 61 septic patients and 10 controls and the SeqStudy cohort of 224 septic patients and 167 controls, reveals a circulating phageome in the plasma of all sampled individuals. Moreover, infection is associated with overrepresentation of pathogen-specific phages, allowing for identification of bacterial pathogens. We find that information on phage diversity enables identification of the bacteria that produced these phages, including pathovariant strains of Escherichia coli. Phage sequences can likewise be used to distinguish between closely related bacterial species such as Staphylococcus aureus, a frequent pathogen, and coagulase-negative Staphylococcus, a frequent contaminant. Phage cell-free DNA may have utility in studying bacterial infections.

  View details for DOI 10.1038/s41564-023-01406-x

  View details for PubMedID 37308590

  View details for PubMedCentralID 5594678

• The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia. Cell host & microbe Schluter, J., Djukovic, A., Taylor, B. P., Yan, J., Duan, C., Hussey, G. A., Liao, C., Sharma, S., Fontana, E., Amoretti, L. A., Wright, R. J., Dai, A., Peled, J. U., Taur, Y., Perales, M. A., Siranosian, B. A., Bhatt, A. S., van den Brink, M. R., Pamer, E. G., Xavier, J. B. 2023

  Abstract

  Longitudinal microbiome data provide valuable insight into disease states and clinical responses, but they are challenging to mine and view collectively. To address these limitations, we present TaxUMAP, a taxonomically informed visualization for displaying microbiome states in large clinical microbiome datasets. We used TaxUMAP to chart a microbiome atlas of 1,870 patients with cancer during therapy-induced perturbations. Bacterial density and diversity were positively associated, but the trend was reversed in liquid stool. Low-diversity states (dominations) remained stable after antibiotic treatment, and diverse communities had a broader range of antimicrobial resistance genes than dominations. When examining microbiome states associated with risk for bacteremia, TaxUMAP revealed that certain Klebsiella species were associated with lower risk for bacteremia localize in a region of the atlas that is depleted in high-risk enterobacteria. This indicated a competitive interaction that was validated experimentally. Thus, TaxUMAP can chart comprehensive longitudinal microbiome datasets, enabling insights into microbiome effects on human health.

  View details for DOI 10.1016/j.chom.2023.05.027

  View details for PubMedID 37329880

• Cancer Demographics and Time-to-Care in Belize. The oncologist Wong, W., Dickerson, J. C., Valtis, Y. K., Habet, M., Bernard, M., Kelly, L., Lattin, J., Garrity, P., Sood, R., Ohanian, A., Chege, M. W., Bhatt, A. S., Huang, F. W., Yacab, R. 2023

  Abstract

  Belize is a middle-income Caribbean country with poorly described cancer epidemiology and no comprehensive cancer care capacity. In 2018, GO, Inc., a US-based NGO, partnered with the Ministry of Health and the national hospital in Belize City to create the first public oncology clinic in the country. Here, we report demographics from the clinic and describe time intervals to care milestones to allow for public health targeting of gaps.Using paper charts and a mobile health platform, we performed a retrospective chart review at the Karl Heusner Memorial Hospital (KHMH) clinic from 2018 to 2022.During this time period, 465 patients with cancer presented to the clinic. Breast cancer (28%) and cervical cancer (12%) were most common. Most patients (68%) presented with stage 3 or 4 disease and were uninsured (78%) and unemployed (79%). Only 21% of patients ever started curative intent treatment. Median time from patient-reported symptoms to a biopsy or treatment was 130 and 189 days. For the most common cancer, breast, similar times were seen at 140 and 178 days. Time intervals at the clinic: <30 days from initial visit to biopsy (if not previously performed) and <30 days to starting chemotherapy.This study reports the first clinic-based cancer statistics for Belize. Many patients have months between symptom onset and treatment. In this setting, the clinic has built infrastructure allowing for minimal delays in care despite an underserved population. This further affirms the need for infrastructure investment and early detection programs to improve outcomes in Belize.

  View details for DOI 10.1093/oncolo/oyad030

  View details for PubMedID 36928719

• Human β-defensin 2 ameliorates acute GVHD by limiting ileal neutrophil infiltration and restraining T cell receptor signaling. Science translational medicine Rückert, T., Andrieux, G., Boerries, M., Hanke-Müller, K., Woessner, N. M., Doetsch, S., Schell, C., Aumann, K., Kolter, J., Schmitt-Graeff, A., Schiff, M., Braun, L. M., Haring, E., Kissel, S., Siranosian, B. A., Bhatt, A. S., Nordkild, P., Wehkamp, J., Jensen, B. A., Minguet, S., Duyster, J., Zeiser, R., Köhler, N. 2022; 14 (676): eabp9675

  Abstract

  Acute graft-versus-host disease (aGVHD), which is driven by allogeneic T cells, has a high mortality rate and limited treatment options. Human β-defensin 2 (hBD-2) is an endogenous epithelial cell-derived host-defense peptide. In addition to its antimicrobial effects, hBD-2 has immunomodulatory functions thought to be mediated by CCR2 and CCR6 in myeloid cells. In this study, we analyzed the effect of recombinant hBD-2 on aGVHD development. We found that intestinal β-defensin expression was inadequately induced in response to inflammation in two independent cohorts of patients with aGVHD and in a murine aGVHD model. Treatment of mice with hBD-2 reduced GVHD severity and mortality and modulated the intestinal microbiota composition, resulting in reduced neutrophil infiltration in the ileum. Furthermore, hBD-2 treatment decreased proliferation and proinflammatory cytokine production by allogeneic T cells in vivo while preserving the beneficial graft-versus-leukemia effect. Using transcriptome and kinome profiling, we found that hBD-2 directly dampened primary murine and human allogeneic T cell proliferation, activation, and metabolism in a CCR2- and CCR6-independent manner by reducing proximal T cell receptor signaling. Furthermore, hBD-2 treatment diminished alloreactive T cell infiltration and the expression of genes involved in T cell receptor signaling in the ilea of mice with aGVHD. Together, we found that both human and murine aGVHD were characterized by a lack of intestinal β-defensin induction and that recombinant hBD-2 represents a potential therapeutic strategy to counterbalance endogenous hBD-2 deficiency.

  View details for DOI 10.1126/scitranslmed.abp9675

  View details for PubMedID 36542690

• Post-Transplant Cyclophosphamide, Tacrolimus, and Mycophenolate Mofetil As the New Standard for Graft-Versus-Host Disease (GVHD) Prophylaxis in Reduced Intensity Conditioning: Results from Phase III BMT CTN 1703 Holtan, S. G., Hamadani, M., Wu, J., Al Malki, M. M., Runaas, L., Elmariah, H., Rezvani, A. R., Gooptu, M., Larkin, K. T., Shaffer, B. C., El Jurdi, N. H., Loren, A. W., Solh, M., Hall, A. C., Alousi, A. M., Jamy, O. H., Perales, M., Yao, J. M., Applegate, K., Bhatt, A. S., Kean, L. S., Efebera, Y. A., Kitko, C., Reshef, R., Clark, W., DiFronzo, N. L., Henderson, L., Jones, R. J., Liefer, E., Martens, M. J., Horowitz, M. M., Bolanos-Meade, J. AMER SOC HEMATOLOGY. 2022: 14-16

  View details for DOI 10.1182/blood-2022-171463

  View details for Web of Science ID 000897957100005

• From genome structure to function: insights into structural variation in microbiology. Current opinion in microbiology West, P. T., Chanin, R. B., Bhatt, A. S. 2022; 69: 102192

  Abstract

  Structural variation in bacterial genomes is an important evolutionary driver. Genomic rearrangements, such as inversions, duplications, and insertions, can regulate gene expression and promote niche adaptation. Importantly, many of these variations are reversible and preprogrammed to generate heterogeneity. While many tools have been developed to detect structural variation in eukaryotic genomes, variation in bacterial genomesand metagenomes remains understudied. However, recent advances in genome sequencing technology and the development of new bioinformatic pipelines hold promise in further understanding microbial genomics.

  View details for DOI 10.1016/j.mib.2022.102192

  View details for PubMedID 36030622

• Near-fatal Legionella pneumonia in a neonate linked to home humidifier by metagenomic next generation sequencing. Med (New York, N.Y.) West, P. T., Brooks, E. F., Costales, C., Moreno, A., Jensen, T. D., Budvytiene, I., Khan, A., Pham, T. H., Schwenk, H. T., Bhatt, A. S., Banaei, N. 2022

  View details for DOI 10.1016/j.medj.2022.06.004

  View details for PubMedID 35863347

• Thousands of small, novel genes predicted in global phage genomes. Cell reports Fremin, B. J., Bhatt, A. S., Kyrpides, N. C. 2022; 39 (12): 110984

  Abstract

  Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.

  View details for DOI 10.1016/j.celrep.2022.110984

  View details for PubMedID 35732113

• Y A pilot study of gut decontamination and the risk of bloodstream infections during pediatric allogeneic hematopoietic cell transplantation Severyn, C. J., Siranosian, B. A., Kong, S., Chen, N., London, W. B., Bhatt, A. S., Whangbo, J. S. WILEY. 2022

  View details for Web of Science ID 000788322300454

• Efficacy of an educational comic book for HPV vaccination information in Nigeria. Roy, M., Saleem, A., Said, A., Inoyo, I. E., Garrity, P., Bashorun, Y., Anjorin, T., Ibeka, P., Remen, D., Huang, F. W., Bhatt, A. LIPPINCOTT WILLIAMS & WILKINS. 2022: E18577

  View details for Web of Science ID 000863680303729

• Breast cancer characteristics and time to chemotherapy initiation in Belize. Wong, W., Dickerson, J., Sood, R., Yacab, R., Valtis, Y., Lattin, J., Garrity, P., Bhatt, A., Huang, F. W. LIPPINCOTT WILLIAMS & WILKINS. 2022: E18643

  View details for Web of Science ID 000863680303792

• Updated demographics at the only public oncology clinic in Belize. Wong, W., Dickerson, J., Sood, R., Valtis, Y., Yacab, R., Lattin, J., Garrity, P., Bhatt, A., Huang, F. W. LIPPINCOTT WILLIAMS & WILKINS. 2022: E18787

  View details for Web of Science ID 000863680303920

• A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients. Scientific data Yan, J., Liao, C., Taylor, B. P., Fontana, E., Amoretti, L. A., Wright, R. J., Littmann, E. R., Dai, A., Waters, N., Peled, J. U., Taur, Y., Perales, M., Siranosian, B. A., Bhatt, A. S., van den Brink, M. R., Pamer, E. G., Schluter, J., Xavier, J. B. 2022; 9 (1): 219

  Abstract

  Hospitalized patients receiving hematopoietic cell transplants provide a unique opportunity to study the human gut microbiome. We previously compiled a large-scale longitudinal dataset of fecal microbiota and associated metadata, but we had limited that analysis to taxonomic composition of bacteria from 16S rRNA gene sequencing. Here we augment those data with shotgun metagenomics. The compilation amounts to a nested subset of 395 samples compiled from different studies at Memorial Sloan Kettering. Shotgun metagenomics describes the microbiome at the functional level, particularly in antimicrobial resistances and virulence factors. We provide accession numbers that link each sample to the paired-end sequencing files deposited in a public repository, which can be directly accessed by the online services of PATRIC to be analyzed without the users having to download or transfer the files. Then, we show how shotgun sequencing enables the assembly of genomes from metagenomic data. The new data, combined with the metadata published previously, enables new functional studies of the microbiomes of patients with cancer receiving bone marrow transplantation.

  View details for DOI 10.1038/s41597-022-01302-9

  View details for PubMedID 35585088

• SARS-CoV-2 RNA and N Antigen Quantification via Wastewater at the Campus Level, Building Cluster Level, and Individual-Building Level ACS ES&T WATER Zambrana, W., Catoe, D., Coffman, M. M., Kim, S., Anand, A., Solis, D., Sahoo, M. K., Pinsky, B. A., Bhatt, A. S., Boehm, A. B., Wolfe, M. K. 2022

  View details for DOI 10.1021/acsestwater.2c00050

  View details for Web of Science ID 000820376800001

• SARS-CoV-2 RNA and N Antigen Quantification via Wastewater at the Campus Level, Building Cluster Level, and Individual-Building Level. ACS ES&T water Zambrana, W., Catoe, D., Coffman, M. M., Kim, S., Anand, A., Solis, D., Sahoo, M. K., Pinsky, B. A., Bhatt, A. S., Boehm, A. B., Wolfe, M. K. 2022; 2 (11): 2025-33

  Abstract

  Monitoring wastewater for SARS-CoV-2 from populations smaller than those served by wastewater treatment plants may help identify small spatial areas (subsewersheds) where COVID-19 infections are present. We sampled wastewater from three nested locations with different sized populations within the same sewer network at a university campus and quantified SARS-CoV-2 RNA using reverse transcriptase droplet digital polymerase chain reaction (PCR). SARS-CoV-2 RNA concentrations and/or concentrations normalized by PMMoV were positively associated with laboratory-confirmed COVID-19 cases for both the sewershed level and the subsewershed level. We also used an antigen-based assay to detect the nucleocapsid (N) antigen from SARS-CoV-2 in wastewater samples at the sewershed level. The N antigen was regularly detected at the sewershed level, but the results were not associated with either laboratory-confirmed COVID-19 cases or SARS-CoV-2 RNA concentrations. The results of this study indicate that wastewater monitoring based on quantification of SARS-CoV-2 RNA using PCR-based methods is associated with COVID-19 cases at multiple geographic scales within the subsewershed level and can serve to aid the public health response.

  View details for DOI 10.1021/acsestwater.2c00050

  View details for PubMedID 37552722

  View details for PubMedCentralID PMC9128006

• Gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA suggest prolonged gastrointestinal infection. Med (New York, N.Y.) Natarajan, A., Zlitni, S., Brooks, E. F., Vance, S. E., Dahlen, A., Hedlin, H., Park, R. M., Han, A., Schmidtke, D. T., Verma, R., Jacobson, K. B., Parsonnet, J., Bonilla, H. F., Singh, U., Pinsky, B. A., Andrews, J. R., Jagannathan, P., Bhatt, A. S. 2022

  Abstract

  COVID-19 manifests with respiratory, systemic, and gastrointestinal (GI) symptoms.1,2 SARS-CoV-2 RNA is detected in respiratory and fecal samples, and recent reports demonstrate viral replication in both the lung and intestinal tissue.3-5 Although much is known about early fecal RNA shedding, little is known about the long term shedding, especially in those with mild COVID-19. Furthermore, most reports of fecal RNA shedding do not correlate these findings with GI symptoms.6.We analyze the dynamics of fecal RNA shedding up to 10 months after COVID-19 diagnosis in 113 individuals with mild to moderate disease. We also correlate shedding with disease symptoms.Fecal SARS-CoV-2 RNA is detected in 49.2% [95% Confidence interval = 38.2%-60.3%] of participants within the first week after diagnosis. Whereas there was no ongoing oropharyngeal SARS-CoV-2 RNA shedding in subjects at and after 4 months, 12.7% [8.5%-18.4%] of participants continued to shed SARS-CoV-2 RNA in the feces at 4 months after diagnosis and 3.8% [2.0%-7.3%] shed at 7 months. Finally, we find that GI symptoms (abdominal pain, nausea, vomiting) are associated with fecal shedding of SARS-CoV-2 RNA.The extended presence of viral RNA in feces, but not respiratory samples, along with the association of fecal viral RNA shedding with GI symptoms suggest that SARS-CoV-2 infects the GI tract, and that this infection can be prolonged in a subset of individuals with COVID-19.

  View details for DOI 10.1016/j.medj.2022.04.001

  View details for PubMedID 35434682

  View details for PubMedCentralID PMC9005383

• Microbiota dynamics in a randomized trial of gut decontamination during allogeneic hematopoietic cell transplantation. JCI insight Severyn, C. J., Siranosian, B. A., Kong, S. T., Moreno, A., Li, M. M., Chen, N., Duncan, C. N., Margossian, S. P., Lehmann, L. E., Sun, S., Andermann, T. M., Birbrayer, O., Silverstein, S., Kim, S., Banaei, N., Ritz, J., Fodor, A. A., London, W. B., Bhatt, A. S., Whangbo, J. S. 2022

  Abstract

  Gut decontamination (GD) can decrease the incidence and severity of acute graft-versus-host-disease (aGVHD) in murine models of allogeneic hematopoietic cell transplantation (HCT). In this pilot study, we examined the impact of GD on the gut microbiome composition and incidence of aGVHD in HCT patients.We randomized 20 pediatric patients undergoing allogeneic HCT to receive (GD) or not receive (no-GD) oral vancomycin-polymyxin B from day -5 through neutrophil engraftment. We evaluated shotgun metagenomic sequencing of serial stool samples to compare the composition and diversity of the gut microbiome between study arms. We assessed clinical outcomes in the 2 arms and performed strain-specific analyses of pathogens that caused bloodstream infections (BSI).The two arms did not differ in the predefined primary outcome of Shannon diversity of the gut microbiome at two weeks post-HCT (Genus, p=0.8; Species, p=0.44) or aGVHD incidence (p=0.58). Immune reconstitution of T-cell and B-cell subsets was similar between groups. Five patients in the no-GD arm had eight BSI episodes vs one episode in the GD arm (p=0.09). The BSI-causing pathogens were traceable to the gut in seven of eight BSI episodes in the no-GD arm, including Staphylococcus species.While GD did not differentially impact Shannon diversity or clinical outcomes, our findings suggest that GD may protect against gut-derived BSI in HCT patients by decreasing the prevalence or abundance of gut pathogens.ClinicalTrials.gov NCT02641236FUNDING. NIH, Damon Runyon Cancer Research Foundation, V Foundation, Sloan Foundation, Emerson Collective, Stanford MCHRI.

  View details for DOI 10.1172/jci.insight.154344

  View details for PubMedID 35239511

• Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa. Nature communications Tamburini, F. B., Maghini, D., Oduaran, O. H., Brewster, R., Hulley, M. R., Sahibdeen, V., Norris, S. A., Tollman, S., Kahn, K., Wagner, R. G., Wade, A. N., Wafawanaka, F., Gomez-Olive, F. X., Twine, R., Lombard, Z., H3Africa AWI-Gen Collaborative Centre, Hazelhurst, S., Bhatt, A. S., Agongo, G., Alberts, M., Ali, S., Asiki, G., Baloyi, V., Boua, P. R., Brandenburg, J., Ceballos, F. C., Chikowore, T., Choma, S., Choudhury, A., Crowther, N., Debpuur, C., Gondwe, M., Hazelhurst, S., Kahn, K., Khayeka-Wandabwa, C., Kisiangani, I., Kyobutungi, C., Lombard, Z., Mashaba, G., Mashinya, F., Mathema, T., Micklesfield, L., Mohamed, S., Mthembu, B., Mukomana, F., Nonterah, E., Norris, S. A., Oduaran, O., Oduro, A. R., Gomez-Olive, F. X., Ramsay, M., Sankoh, O., Sengupta, D., Smyth, N., Soo, C., Soodyall, H., Sorgho, H., Swiel, Y., Tambo, E., Tindana, P., Tinto, H., Tluway, F., Tollman, S., Twine, R., Wade, A., Wagner, R., Wandera, H., Kabudula, C., Ohene-Kwofie, D., Wafawanaka, F. 2022; 13 (1): 926

  Abstract

  Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world's population. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (n=118) or urban Soweto (n=51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple "western-nonwestern" axis andcontains undescribed microbial diversity.

  View details for DOI 10.1038/s41467-021-27917-x

  View details for PubMedID 35194028

• Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults. Nature communications Siranosian, B. A., Brooks, E. F., Andermann, T., Rezvani, A. R., Banaei, N., Tang, H., Bhatt, A. S. 1800; 13 (1): 586

  Abstract

  Bacterial bloodstream infections are a major cause of morbidity and mortality among patients undergoing hematopoietic cell transplantation (HCT). Although previous research has demonstrated that pathogens may translocate from the gut microbiome into the bloodstream to cause infections, the mechanisms by which HCT patients acquire pathogens in their microbiome have not yet been described. Here, we use linked-read and short-read metagenomic sequencing to analyze 401 stool samples collected from 149 adults undergoing HCT and hospitalized in the same unit over three years, many of whom were roommates. We use metagenomic assembly and strain-specific comparison methods to search for high-identity bacterial strains, which may indicate transmission between the gut microbiomes of patients. Overall, the microbiomes of patients who share time and space in the hospital do not converge in taxonomic composition. However, we do observe six pairs of patients who harbor identical or nearly identical strains of the pathogen Enterococcus faecium, or the gut commensals Akkermansia muciniphila andHungatella hathewayi. These shared strains may result from direct transmission between patients who shared a room and bathroom, acquisition from a common hospital source, or transmission from an unsampled intermediate. We also identify multiple patients with identical strains of species commonly found in commercial probiotics, including Lactobacillus rhamnosus and Streptococcus thermophilus. In summary, our findings indicate that sharing of identical pathogens between the gut microbiomes of multiple patients is a rare phenomenon. Furthermore, the observed potential transmission of commensal, immunomodulatory microbes suggests that exposure to other humans may contribute to microbiome reassembly post-HCT.

  View details for DOI 10.1038/s41467-022-28048-7

  View details for PubMedID 35102136

• Microbiota dynamics in a randomized trial of gut decontamination during allogeneic hematopoietic cell transplantation JCI Insight Severyn, C. J., et al 2022

  View details for DOI 10.1172/jci.insight.154344

• MI-Immune/1801: Lessons from an Ongoing, Multi-Center Trial Involving Biospecimen Collection for Prospective Microbiome and Immune Profiling in Patients Undergoing Reduced Intensity Conditioning Allogeneic HCT Brooks, E., Spahn, A., Waldvogel, S., Howard, A., Bar, M., Bratrude, B., Chhabra, S., Clark, W., Das, S., Horowitz, M. M., Jenq, R. R., Jones, R. J., Levine, J. E., Logan, B. R., Murthy, H. S., Rashidi, A., Riches, M. L., Riwes, M., Sandhu, K. S., Sung, A. D., Al Malki, M. M., Runaas, L., Elmariah, H., Rezvani, A. R., Gooptu, M., Bolanos-Meade, J., Holtan, S. G., Saber, W., Hamadani, M., Kean, L. S., Perales, M., Bhatt, A. S. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-149313

  View details for Web of Science ID 000736413904028

• Reporting guidelines for human microbiome research: the STORMS checklist. Nature medicine Mirzayi, C., Renson, A., Genomic Standards Consortium, Massive Analysis and Quality Control Society, Zohra, F., Elsafoury, S., Geistlinger, L., Kasselman, L. J., Eckenrode, K., van de Wijgert, J., Loughman, A., Marques, F. Z., MacIntyre, D. A., Arumugam, M., Azhar, R., Beghini, F., Bergstrom, K., Bhatt, A., Bisanz, J. E., Braun, J., Bravo, H. C., Buck, G. A., Bushman, F., Casero, D., Clarke, G., Collado, M. C., Cotter, P. D., Cryan, J. F., Demmer, R. T., Devkota, S., Elinav, E., Escobar, J. S., Fettweis, J., Finn, R. D., Fodor, A. A., Forslund, S., Franke, A., Furlanello, C., Gilbert, J., Grice, E., Haibe-Kains, B., Handley, S., Herd, P., Holmes, S., Jacobs, J. P., Karstens, L., Knight, R., Knights, D., Koren, O., Kwon, D. S., Langille, M., Lindsay, B., McGovern, D., McHardy, A. C., McWeeney, S., Mueller, N. T., Nezi, L., Olm, M., Palm, N., Pasolli, E., Raes, J., Redinbo, M. R., Ruhlemann, M., Balfour Sartor, R., Schloss, P. D., Schriml, L., Segal, E., Shardell, M., Sharpton, T., Smirnova, E., Sokol, H., Sonnenburg, J. L., Srinivasan, S., Thingholm, L. B., Turnbaugh, P. J., Upadhyay, V., Walls, R. L., Wilmes, P., Yamada, T., Zeller, G., Zhang, M., Zhao, N., Zhao, L., Bao, W., Culhane, A., Devanarayan, V., Dopazo, J., Fan, X., Fischer, M., Jones, W., Kusko, R., Mason, C. E., Mercer, T. R., Sansone, S., Scherer, A., Shi, L., Thakkar, S., Tong, W., Wolfinger, R., Hunter, C., Segata, N., Huttenhower, C., Dowd, J. B., Jones, H. E., Waldron, L., Furlanello, C., Sansone, S. 2021

  Abstract

  The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called 'Strengthening The Organization and Reporting of Microbiome Studies' (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials. The STORMS checklist provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results.

  View details for DOI 10.1038/s41591-021-01552-x

  View details for PubMedID 34789871

• Implementing Patient-Directed Cancer Education Materials Across Nigeria. JCO global oncology Dickerson, J. C., Ibeka, P., Inoyo, I., Oke, O. O., Adewuyi, S. A., Barry, D., Bello, A., Fasawe, O., Garrity, P., Habeebu, M., Huang, F. W., Mulema, V., Nwankwo, K. C., Remen, D., Wiwa, O., Bhatt, A. S., Roy, M. 2021; 7: 1610-1619

  Abstract

  PURPOSE: As access to cancer care expands in low-income countries, developing tools to educate patients is paramount. We took a picture booklet, which was initially developed by the nonprofit Global Oncology for Malawi and Rwanda, and adapted it for use in Nigeria. The primary goal was to assess acceptability and provide education. The secondary goals were (1) to describe the collaboration, (2) to assess knowledge gained from the intervention, (3) to assess patient understanding of their therapy intent, and (4) to explore patient's experiences via qualitative analysis.METHODS: We piloted the original English booklet at a single site and requested feedback from patients and providers. The booklet was updated; translated into Hausa, Yoruba, Igbo, and Pidgin English; and used at three additional sites. For the three-site cohort, we collected basic demographics, pretest and post-test assessing content in the booklet, and performed a qualitative analysis.RESULTS: The original booklet was widely acceptable and recommended by patients at site one (n = 31) and by providers (N = 26) representing all four sites. In the three-site cohort (n = 103), 94% of patients recommended the booklet. An immediate post-test focusing on when patients should present to care showed a statistically significant improvement in one of the seven questions. Fifty-one percent of the patients (n = 103) knew their treatment intent (curative v palliative). Qualitative analysis highlighted that the patient's thoughts on cancer are dominated by negative associations, although curability and modern therapy are also frequently cited.CONCLUSION: We adapted an educational booklet to a novel context and had it delivered by local partners. The booklet was widely recommended to future patients. The booklet had an impact on patient's knowledge of cancer treatment, potentially allowing for decreased abandonment.

  View details for DOI 10.1200/GO.21.00233

  View details for PubMedID 34860566

• Simultaneous ribosome profiling of hundreds of microbes from the human microbiome. Nature protocols Fremin, B. J., Nicolaou, C., Bhatt, A. S. 2021

  Abstract

  Ribosome profiling enables sequencing of ribosome-bound fragments of RNA, revealing which transcripts are being translated as well as the position of ribosomes along mRNAs. Although ribosome profiling has been applied to cultured bacterial isolates, its application to uncultured, mixed communities has been challenging. We present MetaRibo-Seq, a protocol that enables the application of ribosome profiling directly to the human fecal microbiome. MetaRibo-Seq is a benchmarked method that includes several modifications to existing ribosome profiling protocols, specifically addressing challenges involving fecal sample storage, purity and input requirements. We also provide a computational workflow to quality control and trim reads, de novo assemble a reference metagenome with metagenomic reads, align MetaRibo-Seq reads to the reference, and assess MetaRibo-Seq library quality ( https://github.com/bhattlab/bhattlab_workflows/tree/master/metariboseq ). This MetaRibo-Seq protocol enables researchers in standard molecular biology laboratories to study translation in the fecal microbiome in ~5 d.

  View details for DOI 10.1038/s41596-021-00592-4

  View details for PubMedID 34381207

• A fructo-oligosaccharide prebiotic is well-tolerated in adults undergoing allogeneic hematopoietic stem cell transplantation: a phase I dose-escalation trial. Transplantation and cellular therapy Andermann, T. M., Fouladi, F., Tamburini, F. B., Sahaf, B., Tkachenko, E., Greene, C., Buckley, M. T., Brooks, E. F., Hedlin, H., Arai, S., Mackall, C. L., Miklos, D., Negrin, R. S., Fodor, A. A., Rezvani, A. R., Bhatt, A. S. 2021

  Abstract

  BACKGROUND: Alterations of the gut microbiota after allogeneic hematopoietic cell transplantation (allo-HCT) are a key factor in the development of transplant-related complications such as graft-versus-host disease (GVHD). Interventions that preserve the gut microbiome hold promise to improve HCT-associated morbidity and mortality. Murine models demonstrate that prebiotics such as fructo-oligosaccharides (FOS) may increase gut levels of short-chain fatty acids (SCFAs) such as butyrate, and consequently induce proliferation of immunomodulatory FOXP3+ CD4+ T-regulatory cells (Tregs), that impact GVHD risk.METHODS: We conducted a pilot Phase I trial to assess the investigate the maximum tolerated dose of FOS in patients undergoing reduced-intensity (RIC) allo-HCT (n=15) compared to concurrent controls (n=16). We administered FOS starting at pretransplant conditioning and continuing for a total of 21 days. We characterized the gut microbiome using shotgun metagenomic sequencing, measured stool SCFAs using LC-MS, and determined peripheral T-cell concentrations using CyTOF.RESULTS: We found that FOS was safe and well-tolerated at 10g per day without significant adverse effects in patients undergoing allo-HCT. Community-level gut microbiota composition was significantly different on the day of transplant (day 0) between patients receiving FOS compared to concurrent controls, however FOS-associated alterations of the gut microbiota were not sustained after transplant. Although the impact of FOS was fleeting, transplantation itself impacted a substantial number of taxa over time. In our small pilot trial, no significant differences were observed in gut microbial metabolic pathways, stool SCFAs, or in peripheral Tregs although Tregs trended higher in those patients who received FOS. A marker of CD4+ T-cell activation, namely CTLA4+, was significantly higher in patients receiving FOS, whereas a non-significant trend existed for FOP3+CD4+ T-regulatory cells that were higher in those receiving FOS compared to controls.CONCLUSIONS: FOS is well-tolerated at 10g per day in patients undergoing RIC allo-HCT. While alterations in the gut microbiota and peripheral immune cell composition in those receiving FOS are intriguing, additional studies are required to investigate the use of prebiotics in HCT recipients.

  View details for DOI 10.1016/j.jtct.2021.07.009

  View details for PubMedID 34274493

• Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nature microbiology Nayfach, S., Paez-Espino, D., Call, L., Low, S. J., Sberro, H., Ivanova, N. N., Proal, A. D., Fischbach, M. A., Bhatt, A. S., Hugenholtz, P., Kyrpides, N. C. 2021

  Abstract

  Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.

  View details for DOI 10.1038/s41564-021-00928-6

  View details for PubMedID 34168315

• Invariant Natural Killer T Cell Subsets Have Diverse Graft-Versus-Host-Disease-Preventing and Anti-Tumor Effects. Blood Maas-Bauer, K., Lohmeyer, J. K., Hirai, T., Lopes Ramos, T., Fazal, F. M., Litzenburger, U. M., Yost, K. E., Ribado, J. V., Kambham, N., Wenokur, A., Lin, P., Alvarez, M., Mavers, M., Baker, J., Bhatt, A. S., Chang, H., Simonetta, F., Negrin, R. S. 2021

  Abstract

  Invariant Natural Killer T (iNKT) cells are a T cell subset with potent immunomodulatory properties. Experimental evidence in mice and observational studies in humans indicate that iNKT cells have antitumor potential as well as the ability to suppress acute and chronic Graft-versus-Host-Disease (GvHD). Murine iNKT cells differentiate during thymic development into iNKT1, iNKT2 and iNKT17 sublineages, which differ transcriptomically and epigenomically, and have subset-specific developmental requirements. Whether distinct iNKT sublineages also differ in their antitumor effect and their ability to suppress GvHD is currently unknown. In this work, we generated highly purified murine iNKT-sublineages, characterized their transcriptomic and epigenomic landscape, and assessed specific functions. We demonstrate that iNKT2 and iNKT17, but not iNKT1 cells, efficiently suppress T cell activation in vitro and mitigate murine acute GvHD in vivo. Conversely, we show that iNKT1 cells display the highest antitumor activity against murine B-cell lymphoma cells both in vitro and in vivo. Thus, we demonstrate for the first time that iNKT sublineages have distinct and different functions, with iNKT1 cells having the highest antitumor activity and iNKT2 and iNKT17 cells having immune-regulatory properties. These results have important implications for the translation of iNKT cell therapies to the clinic for cancer immunotherapy as well as for GvHD prevention and treatment.

  View details for DOI 10.1182/blood.2021010887

  View details for PubMedID 34036317

• Standardized and optimized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. medRxiv : the preprint server for health sciences Natarajan, A., Han, A., Zlitni, S., Brooks, E. F., Vance, S. E., Wolfe, M., Singh, U., Jagannathan, P., Pinsky, B. A., Boehm, A., Bhatt, A. S. 2021

  Abstract

  COVID-19 patients shed SARS-CoV-2 viral RNA in their stool, sometimes well after they have cleared their respiratory infection. This feature of the disease may be significant for patient health, epidemiology, and diagnosis. However, to date, methods to preserve stool samples from COVID patients, and to extract and quantify viral RNA concentration have yet to be optimized. We sought to meet this urgent need by developing and benchmarking a standardized protocol for the fecal detection of SARS-CoV-2 RNA. We test three preservative conditions for their ability to yield detectable SARS-CoV-2 RNA: OMNIgene-GUT, Zymo DNA/RNA shield kit, and the most common condition, storage without any preservative. We test these in combination with three extraction kits: the QIAamp Viral RNA Mini Kit, Zymo Quick-RNA Viral Kit, and MagMAX Viral/Pathogen Kit. Finally, we also test the utility of two detection methods, ddPCR and RT-qPCR, for the robust quantification of SARS-CoV-2 viral RNA from stool. We identify that the Zymo DNA/RNA shield collection kit and the QiaAMP viral RNA mini kit yield more detectable RNA than the others, using both ddPCR and RT-qPCR assays. We also demonstrate key features of experimental design including the incorporation of appropriate controls and data analysis, and apply these techniques to effectively extract viral RNA from fecal samples acquired from COVID-19 outpatients enrolled in a clinical trial. Finally, we recommend a comprehensive methodology for future preservation, extraction and detection of RNA from SARS-CoV-2 and other coronaviruses in stool.

  View details for DOI 10.1101/2021.04.10.21255250

  View details for PubMedID 33880485

• The Gut Microbiome: A Missing Link in Understanding the Gastrointestinal manifestations of COVID-19? Cold Spring Harbor molecular case studies Brooks, E., Bhatt, A. S. 2021

  Abstract

  Coronavirus disease 2019 (COVID-19), which is caused by infection with SARS-CoV-2, presents with a broad constellation of both respiratory and non-respiratory symptoms, although it is primarily considered a respiratory disease. Gastrointestinal symptoms, including nausea, abdominal pain, vomiting and diarrhea, rank chief among these. When coupled with the presence of viral RNA in fecal samples, the presence of gastrointestinal symptoms raises relevant questions regarding whether SARS-CoV-2 can productively infect the upper or lower gastrointestinal tract. Despite the well-documented prevalence of gastrointestinal symptoms and the high rate of SARS-CoV-2 fecal RNA shedding, the biological, clinical and epidemiological relevance of these findings is unclear. Furthermore, the isolation of replication-competent virus from fecal samples has not been reproducibly and rigorously demonstrated. While SARS-CoV-2 shedding likely occurs in a high proportion of patients, gastrointestinal symptoms affect only a subset of individuals. Herein, we summarize what is known about gastrointestinal symptoms and fecal viral shedding in COVID-19, explore the role of the gut microbiome in other respiratory diseases, speculate on the role of the gut microbiota in COVID-19 and discuss potential future directions. Taking these concepts together, we propose that studying gut microbiota perturbations in COVID-19 will enhance our understanding of the symptomology and pathophysiology of this novel devastating disease.

  View details for DOI 10.1101/mcs.a006031

  View details for PubMedID 33593727

• Peginterferon Lambda-1a for treatment of outpatients with uncomplicated COVID-19: a randomized placebo-controlled trial. Nature communications Jagannathan, P. n., Andrews, J. R., Bonilla, H. n., Hedlin, H. n., Jacobson, K. B., Balasubramanian, V. n., Purington, N. n., Kamble, S. n., de Vries, C. R., Quintero, O. n., Feng, K. n., Ley, C. n., Winslow, D. n., Newberry, J. n., Edwards, K. n., Hislop, C. n., Choong, I. n., Maldonado, Y. n., Glenn, J. n., Bhatt, A. n., Blish, C. n., Wang, T. n., Khosla, C. n., Pinsky, B. A., Desai, M. n., Parsonnet, J. n., Singh, U. n. 2021; 12 (1): 1967

  Abstract

  Type III interferons have been touted as promising therapeutics in outpatients with coronavirus disease 2019 (COVID-19). We conducted a randomized, single-blind, placebo-controlled trial (NCT04331899) in 120 outpatients with mild to moderate COVID-19 to determine whether a single, 180 mcg subcutaneous dose of Peginterferon Lambda-1a (Lambda) within 72 hours of diagnosis could shorten the duration of viral shedding (primary endpoint) or symptoms (secondary endpoint). In both the 60 patients receiving Lambda and 60 receiving placebo, the median time to cessation of viral shedding was 7 days (hazard ratio [HR] = 0.81; 95% confidence interval [CI] 0.56 to 1.19). Symptoms resolved in 8 and 9 days in Lambda and placebo, respectively, and symptom duration did not differ significantly between groups (HR 0.94; 95% CI 0.64 to 1.39). Both Lambda and placebo were well-tolerated, though liver transaminase elevations were more common in the Lambda vs. placebo arm (15/60 vs 5/60; p = 0.027). In this study, a single dose of subcutaneous Peginterferon Lambda-1a neither shortened the duration of SARS-CoV-2 viral shedding nor improved symptoms in outpatients with uncomplicated COVID-19.

  View details for DOI 10.1038/s41467-021-22177-1

  View details for PubMedID 33785743

• Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. Nature communications Natarajan, A., Han, A., Zlitni, S., Brooks, E. F., Vance, S. E., Wolfe, M., Singh, U., Jagannathan, P., Pinsky, B. A., Boehm, A., Bhatt, A. S. 2021; 12 (1): 5753

  Abstract

  Patients with COVID-19 shed SARS-CoV-2 RNA in stool, sometimes well after their respiratory infection has cleared. This may be significant for patient health, epidemiology, and diagnosis. However, methods to preserve stool, and to extract and quantify viral RNA are not standardized. We test the performance of three preservative approaches at yielding detectable SARS-CoV-2 RNA: the OMNIgene-GUT kit, Zymo DNA/RNA shield kit, and the most commonly applied, storage without preservative. We test these in combination with three extraction kits: QIAamp Viral RNA Mini Kit, Zymo Quick-RNA Viral Kit, and MagMAX Viral/Pathogen Kit. We also test the utility of ddPCR and RT-qPCR for the reliable quantification of SARS-CoV-2 RNA from stool. We identify that the Zymo DNA/RNA preservative and the QiaAMP extraction kit yield more detectable RNA than the others, using both ddPCR and RT-qPCR. Taken together, we recommend a comprehensive methodology for preservation, extraction and detection of RNA from SARS-CoV-2 and other coronaviruses in stool.

  View details for DOI 10.1038/s41467-021-25576-6

  View details for PubMedID 34599164

• Identification of covalent inhibitors that disrupt M. tuberculosis growth by targeting multiple serine hydrolases involved in lipid metabolism. Cell chemical biology Babin, B. M., Keller, L. J., Pinto, Y., Li, V. L., Eneim, A. S., Vance, S. E., Terrell, S. M., Bhatt, A. S., Long, J. Z., Bogyo, M. 2021

  Abstract

  The increasing incidence of antibiotic-resistant Mycobacterium tuberculosis infections is a global health threat necessitating the development of new antibiotics. Serine hydrolases (SHs) are a promising class of targets because of their importance for the synthesis of the mycobacterial cell envelope. We screen a library of small molecules containing serine-reactive electrophiles and identify narrow-spectrum inhibitors of M. tuberculosis growth. Using these lead molecules, we perform competitive activity-based protein profiling and identify multiple SH targets, including enzymes with uncharacterized functions. Lipidomic analyses of compound-treated cultures reveal an accumulation of free lipids and a substantial decrease in lipooligosaccharides, linking SH inhibition to defects in cell envelope biogenesis. Mutant analysis reveals a path to resistance via the synthesis of mycocerates, but not through mutations to SH targets. Our results suggest that simultaneous inhibition of multiple SH enzymes is likely to be an effective therapeutic strategy for the treatment of M. tuberculosis infections.

  View details for DOI 10.1016/j.chembiol.2021.08.013

  View details for PubMedID 34599874

• Comparative genomics of Enterobacter cloacae complex before and after acquired clinical resistance to Ceftazidime-Avibactam. Diagnostic microbiology and infectious disease Senchyna, F., Tamburini, F. B., Murugesan, K., Watz, N., Bhatt, A. S., Banaei, N. 2021; 101 (4): 115511

  Abstract

  Resistance to Ceftazidime-Avibactam in Enterobacter cloacae is poorly understood. Whole genome sequencing identified 6 variants in isolates collected from a patient before and after acquiring Ceftazidime-Avibactam resistance. This included a Phe396Leu mutation in acrB, a component of the AcrAB-TolC efflux pump, possibly mediating enhanced efflux of Ceftazidime and/ or Avibactam.

  View details for DOI 10.1016/j.diagmicrobio.2021.115511

  View details for PubMedID 34418822

• Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes. Genome biology Fremin, B. J., Bhatt, A. S. 2021; 22 (1): 100

  Abstract

  Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. The human microbiome contains thousands of species and strains of microbes. Yet, much of the metagenomic data from the human microbiome remains unmined for structured RNA motifs primarily due to computational limitations.We sought to apply a large-scale, comparative genomics approach to these organisms to identify candidate structured RNAs. With a carefully constructed, though computationally intensive automated analysis, we identify 3161 conserved candidate structured RNAs in intergenic regions, as well as 2022 additional candidate structured RNAs that may overlap coding regions. We validate the RNA expression of 177 of these candidate structures by analyzing small fragment RNA-seq data from four human fecal samples.This approach identifies a wide variety of candidate structured RNAs, including tmRNAs, antitoxins, and likely ribosome protein leaders, from a wide variety of taxa. Overall, our pipeline enables conservative predictions of thousands of novel candidate structured RNAs from human microbiomes.

  View details for DOI 10.1186/s13059-021-02319-w

  View details for PubMedID 33845850

• Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition. BMC microbiology Oduaran, O. H., Tamburini, F. B., Sahibdeen, V., Brewster, R., Gomez-Olive, F. X., Kahn, K., Norris, S. A., Tollman, S. M., Twine, R., Wade, A. N., Wagner, R. G., Lombard, Z., Bhatt, A. S., Hazelhurst, S. 2020; 20 (1): 330

  Abstract

  BACKGROUND: Comparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition. Yet, little is known about the gut microbiome composition of most communities in the very diverse African continent. South Africa comprises a richly diverse ethnolinguistic population that is experiencing an ongoing epidemiological transition and concurrent spike in the prevalence of obesity, largely attributed to a shift towards more Westernized diets and increasingly inactive lifestyle practices. To characterize the microbiome of African adults living in more mainstream lifestyle settings and investigate associations between the microbiome and obesity, we conducted a pilot study, designed collaboratively with community leaders, in two South African cohorts representative of urban and transitioning rural populations. As the rate of overweight and obesity is particularly high in women, we collected single time-point stool samples from 170 HIV-negative women (51 at Soweto; 119 at Bushbuckridge), performed 16S rRNA gene sequencing on these samples and compared the data to concurrently collected anthropometric data.RESULTS: We found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, we find that geographical location was more important for sample clustering than lean/obese status and observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in Bushbuckridge. Also, Prevotella, despite its generally high prevalence in the cohorts, showed an association with obesity. In comparisons with benchmarked datasets representative of non-Western populations, relatively higher abundance values were observed in our dataset for Barnesiella (log2fold change (FC)=4.5), Alistipes (log2FC=3.9), Bacteroides (log2FC=4.2), Parabacteroides (log2FC=3.1) and Treponema (log2FC=1.6), with the exception of Prevotella (log2FC=-4.7).CONCLUSIONS: Altogether, this work identifies putative microbial features associated with host health in a historically understudied community undergoing an epidemiological transition. Furthermore, we note the crucial role of community engagement to the success of a study in an African setting, the importance of more population-specific studies to inform targeted interventions as well as present a basic foundation for future research.

  View details for DOI 10.1186/s12866-020-02017-w

  View details for PubMedID 33129264

• Recommendations from the ASCO Academic Global Oncology Task Force. JCO global oncology Gralow, J. R., Asirwa, F. C., Bhatt, A. S., Bourlon, M. T., Chu, Q., Eniu, A. E., Loehrer, P. J., Lopes, G., Shulman, L. N., Close, J., Von Roenn, J., Tibbits, M., Pyle, D. 2020; 6: 1666–73

  Abstract

  In recognition of the rising incidence and mortality of cancer in low- and middle-resource settings, as well as the increasingly international profile of its membership, ASCO has prioritized efforts to enhance its engagement at a global level. Among the recommendations included in the 2016 Global Oncology Leadership Task Force report to the ASCO Board of Directors was that ASCO should promote the recognition of global oncology as an academic field. The report suggested that ASCO could serve a role in transitioning global oncology from an informal field of largely voluntary activities to a more formal discipline with strong research and well-defined training components. As a result of this recommendation, in 2017, ASCO formed the Academic Global Oncology Task Force (AGOTF) to guide ASCO's contributions toward formalizing the field of global oncology. The AGOTF was asked to collect and analyze key issues and barriers toward the recognition of global oncology as an academic discipline, with an emphasis on training, research, and career pathways, and produce a set of recommendations for ASCO action. The outcome of the AGOTF was the development of recommendations designed to advance the status of global oncology as an academic discipline.

  View details for DOI 10.1200/GO.20.00497

  View details for PubMedID 33151772

• Glucagon like peptide-2 for Intestinal stem cell and Paneth cell repair during graft-versus-host disease in mice and humans. Blood Norona, J., Apostolova, P., Schmidt, D., Ihlemann, R., Reischmann, N., Taylor, G., Kohler, N., de Heer, J., Heeg, S., Andrieux, G., Siranosian, B. A., Schmitt-Graeff, A., Pfeifer, D., Catalano, A., Frew, I., Proietti, M., Grimbacher, B., Bulashevska, A., Bhatt, A. S., Brummer, T., Clauditz, T. S., Zabelina, T., Kroeger, N., Blazar, B. R., Boerries, M., Ayuk, F., Zeiser, R. 2020

  Abstract

  Acute graft-versus-host disease (GVHD) is a life-threatening complication after allogeneic hematopoietic cell transplantation (allo-HCT). While currently used GVHD treatment regimens target the donor immune system, we explored here an approach that aims at protecting and regenerating Paneth cells (PC) and intestinal stem cells (ISC). Glucagon-like-peptide-2 (GLP-2) is an enteroendocrine tissue hormone, produced by intestinal L-cells. We observed that acute GVHD reduced intestinal GLP-2 levels in mice and patients developing GVHD. Treatment with the GLP-2 agonist, teduglutide, reduced de novo acute GVHD and steroid-refractory GVHD, without compromising graft-versus-leukemia (GVL) effects in multiple mouse models. Mechanistically GLP-2 substitution promoted regeneration of PCs and ISCs which enhanced production of antimicrobial peptides and caused microbiome changes. GLP-2 expanded intestinal organoids and reduced expression of apoptosis-related genes. Low numbers of L-cells in intestinal biopsies and high serum levels of GLP-2 were associated with higher incidence of non-relapse mortality in patients undergoing allo-HCT. Our findings indicate that L-cells are a target of GVHD and that GLP-2-based treatment of acute GVHD restores intestinal homeostasis via an increase of ISCs and PCs without impairing GVL effects. Teduglutide could become a novel combination partner for immunosuppressive GVHD therapy to be tested in clinical trials.

  View details for DOI 10.1182/blood.2020005957

  View details for PubMedID 32542357

• GUT DECONTAMINATION ALTERS THE INTESTINAL MICROBIOTA DURING ALLOGENIC BONE MARROW TRANSPLANT Severyn, C., London, W., Kao, P., Silverstein, S., Li, M., Verrill, K., Ritz, J., Bhatt, A., Whangbo, J. WILEY. 2020: S11–S12

  View details for Web of Science ID 000530720700020

• Assessing and Addressing the Need for Cancer Patient Education in a Resource-Limited Setting in Haiti. The oncologist Schleimer, L. E., Desameau, P., Damuse, R., Olsen, M., Manzo, V., Cardenas, C., Mehrtash, H., Krakauer, E. L., Masamba, L., Wang, C., Bhatt, A. S., Shulman, L. N., Huang, F. W. 2020

  Abstract

  PURPOSE: Misinformation and lack of information about cancer and its treatment pose significant challenges to delivering cancer care in resource-limited settings and may undermine patient engagement in care. We aimed to investigate patients' knowledge and attitudes toward cancer and its treatment and to adapt, implement, and evaluate a low-literacy cancer patient education booklet at the Hopital Universitaire de Mirebalais (HUM) in rural Haiti.MATERIALS AND METHODS: A low-literacy cancer patient education booklet was adapted into Haitian Creole in collaboration with clinicians at HUM. Patients were recruited for structured interviews (n =20) and two focus groups (n =13) designed to explore patients' attitudes toward cancer and its treatment and to assess whether the booklet increased patients' knowledge via an investigator-designed knowledge test.RESULTS: Participants reported a subjective lack of knowledge about cancer and its treatments and described views of cancer as deadly or incurable. Patients of varying education levels valued receiving written materials that set expectations about cancer treatment and expressed a desire to share the booklet with caregivers and others in their community. Participants across all levels of education significantly increased their performance on a knowledge test after counseling using the booklet (p < .001).CONCLUSION: We found that an educational booklet about cancer developed in collaboration with local providers was well received by patients with variable literacy levels and improved their knowledge of cancer and its treatment in a resource-limited setting. Such educational materials have the potential to serve as tools to engage patients with cancer and their families in care.IMPLICATIONS FOR PRACTICE: Misinformation and lack of information pose significant challenges to delivering cancer care in resource-limited settings; however, there are often no culturally and literacy appropriate tools available to aid in patient education. This article shows that written educational materials are well received by patients of variable literacy levels and can be effective tools for increasing patients' knowledge of cancer and its treatment in a limited-resource setting. Furthermore, we have made our educational booklet, Cancer and You, freely available online and welcome the opportunity to connect with readers of The Oncologist interested in implementing this educational booklet in clinical care.

  View details for DOI 10.1634/theoncologist.2019-0258

  View details for PubMedID 32335989

• The gastrointestinal microbiota controls cancer cell intrinsic mechanisms to promote the progression of acute lymphoblastic leukemia. Mahauad-Fernandez, W., Zlitni, S., Bhatt, A., Felsher, D. AMER ASSOC CANCER RESEARCH. 2020: 58–59

  View details for Web of Science ID 000526057000081

• Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages. Nature communications Siranosian, B. A., Tamburini, F. B., Sherlock, G. n., Bhatt, A. S. 2020; 11 (1): 280

  Abstract

  CrAss-like phages are double-stranded DNA viruses that are prevalent in human gut microbiomes. Here, we analyze gut metagenomic data from mother-infant pairs and patients undergoing fecal microbiota transplantation to evaluate the patterns of acquisition, transmission and strain diversity of crAss-like phages. We find that crAss-like phages are rarely detected at birth but are increasingly prevalent in the infant microbiome after one month of life. We observe nearly identical genomes in 50% of cases where the same crAss-like clade is detected in both the mother and the infant, suggesting vertical transmission. In cases of putative transmission of prototypical crAssphage (p-crAssphage), we find that a subset of strains present in the mother are detected in the infant, and that strain diversity in infants increases with time. Putative tail fiber proteins are enriched for nonsynonymous strain variation compared to other genes, suggesting a potential evolutionary benefit to maintaining strain diversity in specific genes. Finally, we show that p-crAssphage can be acquired through fecal microbiota transplantation.

  View details for DOI 10.1038/s41467-019-14103-3

  View details for PubMedID 31941900

• Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes. Cell host & microbe Durrant, M. G., Bhatt, A. S. 2020

  Abstract

  Small open reading frames (smORFs) and their encoded microproteins play central roles in microbes. However, there is a vast unexplored space of smORFs within human-associated microbes. A recent bioinformatic analysis used evolutionary conservation signals to enhance prediction of small protein families. To facilitate the annotation of specific smORFs, we introduce SmORFinder. This tool combines profile hidden Markov models of each smORF family and deep learning models that better generalize to smORF families not seen in the training set, resulting in predictions enriched for Ribo-seq translation signals. Feature importance analysis reveals that the deep learning models learn to identify Shine-Dalgarno sequences, deprioritize the wobble position in each codon, and group codon synonyms found in the codon table. A core-genome analysis of 26 bacterial species identifies several core smORFs of unknown function. We pre-compute smORF annotations for thousands of RefSeq isolate genomes and Human Microbiome Project metagenomes and provide these data through a public web portal.

  View details for DOI 10.1016/j.chom.2020.11.002

  View details for PubMedID 33290720

• Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome. Nature protocols Maghini, D. G., Moss, E. L., Vance, S. E., Bhatt, A. S. 2020

  Abstract

  Short-read metagenomic sequencing and de novo genome assembly of the human gut microbiome can yield draft bacterial genomes without isolation and culture. However, bacterial genomes assembled from short-read sequencing are often fragmented. Furthermore, these metagenome-assembled genomes often exclude repeated genomic elements, such as mobile genetic elements, compromising our understanding of the contribution of these elements to important bacterial phenotypes. Although long-read sequencing has been applied successfully to the assembly of contiguous bacterial isolate genomes, extraction of DNA of sufficient molecular weight, purity and quantity for metagenomic sequencing from stool samples can be challenging. Here, we present a protocol for the extraction of microgram quantities of high-molecular-weight DNA from human stool samples that are suitable for downstream long-read sequencing applications. We also present Lathe ( www.github.com/bhattlab/lathe ), a computational workflow for long-read basecalling, assembly, consensus refinement with long reads or Illumina short reads and genome circularization. Altogether, this protocol can yield high-quality contiguous or circular bacterial genomes from a complex human gut sample in approximately 10 d, with 2 d of hands-on bench and computational effort.

  View details for DOI 10.1038/s41596-020-00424-x

  View details for PubMedID 33277629

• Structured RNA Contaminants in Bacterial Ribo-Seq. mSphere Fremin, B. J., Bhatt, A. S. 2020; 5 (5)

  Abstract

  Ribosome profiling (Ribo-Seq) is a powerful method to study translation in bacteria. However, Ribo-Seq signal can be observed across RNAs that one would not expect to be bound by ribosomes. For example, Escherichia coli Ribo-Seq libraries also capture reads from most noncoding RNAs (ncRNAs). While some of these ncRNAs may overlap coding regions, this alone does not explain the majority of observed signal across ncRNAs. These fragments of ncRNAs in Ribo-Seq data pass all size selection steps of the Ribo-Seq protocol and survive hours of micrococcal nuclease (MNase) treatment. In this work, we specifically focus on Ribo-Seq signal across ncRNAs and provide evidence to suggest that RNA structure, as opposed to ribosome binding, protects them from degradation and allows them to persist in the Ribo-Seq sequencing library preparation. By inspecting these "contaminant reads" in bacterial Ribo-Seq, we show that data previously disregarded in bacterial Ribo-Seq experiments may, in fact, be used to gain partial information regarding the in vivo secondary structure of ncRNAs.IMPORTANCE Structured ncRNAs are pivotal mediators of bioregulation in bacteria, and their functions are often reliant on their specific structures. Here, we first inspect Ribo-Seq reads across noncoding regions, identifying contaminant reads in these libraries. We observe that contaminant reads in bacterial Ribo-Seq experiments that are often disregarded, in fact, strongly overlap with structured regions of ncRNAs. We then perform several bioinformatic analyses to determine why these contaminant reads may persist in Ribo-Seq libraries. Finally, we highlight some structured RNA contaminants in Ribo-Seq and support the hypothesis that structures in the RNA protect them from MNase digestion. We conclude that researchers should be cautious when interpreting Ribo-Seq signal as coding without considering signal distribution. These findings also may enable us to partially resolve RNA structures, identify novel structured RNAs, and elucidate RNA structure-function relationships in bacteria at a large scale and in vivo through the reanalysis of existing Ribo-Seq data sets.

  View details for DOI 10.1128/mSphere.00855-20

  View details for PubMedID 33087519

• Microbes and microbiomes in 2020 and beyond. Nature communications Natarajan, A. n., Bhatt, A. S. 2020; 11 (1): 4988

  View details for DOI 10.1038/s41467-020-18850-6

  View details for PubMedID 33020496

• MetaRibo-Seq measures translation in microbiomes. Nature communications Fremin, B. J., Sberro, H. n., Bhatt, A. S. 2020; 11 (1): 3268

  Abstract

  No method exists to measure large-scale translation of genes in uncultured organisms in microbiomes. To overcome this limitation, we develop MetaRibo-Seq, a method for simultaneous ribosome profiling of tens to hundreds of organisms in microbiome samples. MetaRibo-Seq was benchmarked against gold-standard Ribo-Seq in a mock microbial community and applied to five different human fecal samples. Unlike RNA-Seq, Ribo-Seq signal of a predicted gene suggests it encodes a translated protein. We demonstrate two applications of this technique: First, MetaRibo-Seq identifies small genes, whose identification until now has been challenging. For example, MetaRibo-Seq identifies 2,091 translated, previously unannotated small protein families from five fecal samples, more than doubling the number of small proteins predicted to exist in this niche. Second, the combined application of RNA-Seq and MetaRibo-Seq identifies differences in the translation of transcripts. In summary, MetaRibo-Seq enables comprehensive translational profiling in microbiomes and identifies previously unannotated small proteins.

  View details for DOI 10.1038/s41467-020-17081-z

  View details for PubMedID 32601270

• Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale. Genome medicine Zlitni, S. n., Bishara, A. n., Moss, E. L., Tkachenko, E. n., Kang, J. B., Culver, R. N., Andermann, T. M., Weng, Z. n., Wood, C. n., Handy, C. n., Ji, H. P., Batzoglou, S. n., Bhatt, A. S. 2020; 12 (1): 50

  Abstract

  Populations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo genome assembly approach that uses read cloud sequencing to provide more complete microbial genome drafts, enabling precise differentiation and tracking of strain-level dynamics across metagenomic samples. In this case study, we present a proof-of-concept using read cloud sequencing to describe bacterial strain diversity in the gut microbiome of one hematopoietic cell transplantation patient over a 2-month time course and highlight temporal strain variation of gut microbes during therapy. The treatment was accompanied by diet changes and administration of multiple immunosuppressants and antimicrobials.We conducted short-read and read cloud metagenomic sequencing of DNA extracted from four longitudinal stool samples collected during the course of treatment of one hematopoietic cell transplantation (HCT) patient. After applying read cloud metagenomic assembly to discover strain-level sequence variants in these complex microbiome samples, we performed metatranscriptomic analysis to investigate differential expression of antibiotic resistance genes. Finally, we validated predictions from the genomic and metatranscriptomic findings through in vitro antibiotic susceptibility testing and whole genome sequencing of isolates derived from the patient stool samples.During the 56-day longitudinal time course that was studied, the patient's microbiome was profoundly disrupted and eventually dominated by Bacteroides caccae. Comparative analysis of B. caccae genomes obtained using read cloud sequencing together with metagenomic RNA sequencing allowed us to identify differences in substrain populations over time. Based on this, we predicted that particular mobile element integrations likely resulted in increased antibiotic resistance, which we further supported using in vitro antibiotic susceptibility testing.We find read cloud assembly to be useful in identifying key structural genomic strain variants within a metagenomic sample. These strains have fluctuating relative abundance over relatively short time periods in human microbiomes. We also find specific structural genomic variations that are associated with increased antibiotic resistance over the course of clinical treatment.

  View details for DOI 10.1186/s13073-020-00747-0

  View details for PubMedID 32471482

• A mountable toilet system for personalized health monitoring via the analysis of excreta. Nature biomedical engineering Park, S. M., Won, D. D., Lee, B. J., Escobedo, D. n., Esteva, A. n., Aalipour, A. n., Ge, T. J., Kim, J. H., Suh, S. n., Choi, E. H., Lozano, A. X., Yao, C. n., Bodapati, S. n., Achterberg, F. B., Kim, J. n., Park, H. n., Choi, Y. n., Kim, W. J., Yu, J. H., Bhatt, A. M., Lee, J. K., Spitler, R. n., Wang, S. X., Gambhir, S. S. 2020

  Abstract

  Technologies for the longitudinal monitoring of a person's health are poorly integrated with clinical workflows, and have rarely produced actionable biometric data for healthcare providers. Here, we describe easily deployable hardware and software for the long-term analysis of a user's excreta through data collection and models of human health. The 'smart' toilet, which is self-contained and operates autonomously by leveraging pressure and motion sensors, analyses the user's urine using a standard-of-care colorimetric assay that traces red-green-blue values from images of urinalysis strips, calculates the flow rate and volume of urine using computer vision as a uroflowmeter, and classifies stool according to the Bristol stool form scale using deep learning, with performance that is comparable to the performance of trained medical personnel. Each user of the toilet is identified through their fingerprint and the distinctive features of their anoderm, and the data are securely stored and analysed in an encrypted cloud server. The toilet may find uses in the screening, diagnosis and longitudinal monitoring of specific patient populations.

  View details for DOI 10.1038/s41551-020-0534-9

  View details for PubMedID 32251391

• A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation. Cell host & microbe Durrant, M. G., Li, M. M., Siranosian, B. A., Montgomery, S. B., Bhatt, A. S. 2019

  Abstract

  Mobile genetic elements (MGEs) contribute to bacterial adaptation and evolution; however, high-throughput, unbiased MGE detection remains challenging. We describe MGEfinder, a bioinformatic toolbox that identifies integrative MGEs and their insertion sites by using short-read sequencing data. MGEfinder identifies the genomic site of each MGE insertion and infers the identity of the inserted sequence. We apply MGEfinder to 12,374 sequenced isolates of 9 prevalent bacterial pathogens, includingMycobacterium tuberculosis, Staphylococcus aureus, and Escherichia coli, and identify thousands of MGEs, including candidate insertion sequences, conjugative transposons, and prophage elements. The MGE repertoire and insertion rates vary across species, and integration sites often cluster near genes related to antibiotic resistance, virulence, and pathogenicity. MGE insertions likely contribute to antibiotic resistance in laboratory experiments and clinical isolates. Additionally, we identified thousands of mobility genes, a subset of which have unknown function opening avenues for exploration. Future application of MGEfinder to commensal bacteria will further illuminate bacterial adaptation and evolution.

  View details for DOI 10.1016/j.chom.2019.10.022

  View details for PubMedID 31862382

• Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly. BMC bioinformatics Kang, J. B., Siranosian, B. A., Moss, E. L., Banaei, N., Andermann, T. M., Bhatt, A. S. 2019; 20 (Suppl 16): 585

  Abstract

  BACKGROUND: Low diversity of the gut microbiome, often progressing to the point of intestinal domination by a single species, has been linked to poor outcomes in patients undergoing hematopoietic cell transplantation (HCT). Our ability to understand how certain organisms attain intestinal domination over others has been restricted in part by current metagenomic sequencing technologies that are typically unable to reconstruct complete genomes for individual organisms present within a sequenced microbial community. We recently developed a metagenomic read cloud sequencing and assembly approach that generates improved draft genomes for individual organisms compared to conventional short-read sequencing and assembly methods. Herein, we applied metagenomic read cloud sequencing to four stool samples collected longitudinally from an HCT patient preceding treatment and over the course of heavy antibiotic exposure.RESULTS: Characterization of microbiome composition by taxonomic classification of reads reveals that that upon antibiotic exposure, the subject's gut microbiome experienced a marked decrease in diversity and became dominated by Escherichia coli. While diversity is restored at the final time point, this occurs without recovery of the original species and strain-level composition. Draft genomes for individual organisms within each sample were generated using both read cloud and conventional assembly. Read clouds were found to improve the completeness and contiguity of genome assemblies compared to conventional assembly. Moreover, read clouds enabled the placement of antibiotic resistance genes present in multiple copies both within a single draft genome and across multiple organisms. The occurrence of resistance genes associates with the timing of antibiotics administered to the patient, and comparative genomic analysis of the various intestinal E. coli strains across time points as well as the bloodstream isolate showed that the subject's E. coli bloodstream infection likely originated from the intestine. The E. coli genome from the initial pre-transplant stool sample harbors 46 known antimicrobial resistance genes, while all other species from the pre-transplant sample each contain at most 5 genes, consistent with a model of heavy antibiotic exposure resulting in selective outgrowth of the highly antibiotic-resistant E. coli.CONCLUSION: This study demonstrates the application and utility of metagenomic read cloud sequencing and assembly to study the underlying strain-level genomic factors influencing gut microbiome dynamics under extreme selective pressures in the clinical context of HCT.

  View details for DOI 10.1186/s12859-019-3073-1

  View details for PubMedID 31787070

• Longitudinal Changes in the Intestinal Microbiome Composition Following Gut Decontamination in Pediatric Allogeneic Hematopoietic Stem Cell Transplant Patients: A Pilot Study Severyn, C., London, W. B., Kao, P., Silverstein, S., Li, M., Kim, S., Verrill, K., Ritz, J., Bhatt, A. S., Whangbo, J. AMER SOC HEMATOLOGY. 2019

  View details for DOI 10.1182/blood-2019-122480

  View details for Web of Science ID 000577164607054

• Making Progress in Graft-Versus-Host Disease Prophylaxis and Microbiome Analysis in the Blood and Marrow Transplant Clinical Trials Network: Progress III (1703)/MI-Immune (1801) Holtan, S., Bhatt, A. S., Fraser, R., Perales, M., Kean, L., Saber, W., Hamadani, M., Logan, B. R., Bolanos-Meade, J. AMER SOC HEMATOLOGY. 2019

  View details for DOI 10.1182/blood-2019-122782

  View details for Web of Science ID 000577160403278

• Microbiome genome structure drives function. Nature microbiology Durrant, M. G., Bhatt, A. S. 2019; 4 (6): 912–13

  View details for DOI 10.1038/s41564-019-0473-y

  View details for PubMedID 31118502

• Making the microbiome personal NATURE MEDICINE Bhatt, A. S. 2019; 25 (5): 708

  View details for DOI 10.1038/s41591-019-0445-z

  View details for Web of Science ID 000468247800003

• Diversity of resistance mechanisms in carbapenem-resistant Enterobacteriaceae at a health care system in Northern California, from 2013 to 2016 DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE Senchyna, F., Gaur, R. L., Sandlund, J., Truong, C., Tremintin, G., Kutz, D., Gomez, C. A., Tamburini, F. B., Andermann, T., Bhatt, A., Tickler, I., Watz, N., Budvytiene, I., Shi, G., Tenover, F. C., Banaei, N. 2019; 93 (3): 250–57

  View details for DOI 10.1016/j.diagmicrobio.2018.10.004

  View details for Web of Science ID 000460196900013

• Distinct Immune Regulatory Potential of Invariant Natural Killer T (iNKT) Cell Subsets: iNKT2 and iNKT17, but Not iNKT1, Protect from Graft-Versus-Host-Disease Simonetta, F., Maas-Bauer, K., Hirai, T., Wenokur, A., Fazal, F. M., Kambham, N., Ribado, J., Mavers, M., Baker, J., Bhatt, A. S., Chang, H. Y., Negrin, R. S. ELSEVIER SCIENCE INC. 2019

  View details for Web of Science ID 000540655500003

• Whole blood RNA sequencing reveals a unique transcriptomic profile in patients with ARDS following hematopoietic stem cell transplantation. Respiratory research Englert, J. A., Cho, M. H., Lamb, A. E., Shumyatcher, M., Barragan-Bradford, D., Basil, M. C., Higuera, A., Isabelle, C., Vera, M. P., Dieffenbach, P. B., Fredenburgh, L. E., Kang, J. B., Bhatt, A. S., Antin, J. H., Ho, V. T., Soiffer, R. J., Howrylak, J. A., Himes, B. E., Baron, R. M. 2019; 20 (1): 15

  Abstract

  BACKGROUND: The acute respiratory distress syndrome (ARDS) is characterized by the acute onset of hypoxemia and bilateral lung infiltrates in response to an inciting event, and is associated with high morbidity and mortality. Patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT) are at increased risk for ARDS. We hypothesized that HSCT patients with ARDS would have a unique transcriptomic profile identifiable in peripheral blood compared to those that did not undergo HSCT.METHODS: We isolated RNA from banked peripheral blood samples from a biorepository of critically ill ICU patients. RNA-Seqwas performed on 11 patients with ARDS (5 that had undergone HSCT and 6 that had not) and 12 patients with sepsis without ARDS (5 that that had undergone HCST and 7 that had not).RESULTS: We identified 687 differentially expressed genes between ARDS and ARDS-HSCT (adjusted p-value <0.01), including IFI44L, OAS3, LY6E, and SPATS2L that had increased expression in ARDS vs. ARDS-HSCT; these genes were not differentially expressed in sepsis vs sepsis-HSCT. Gene ontology enrichment analysis revealed that many differentially expressed genes were related to response to type I interferon.CONCLUSIONS: Our findings reveal significant differences in whole blood transcriptomic profiles of patients with non-HSCT ARDS compared to ARDS-HSCT patients and point toward different immune responses underlying ARDS and ARDS-HSCT that contribute to lung injury.

  View details for PubMedID 30665420

• Whole blood RNA sequencing reveals a unique transcriptomic profile in patients with ARDS following hematopoietic stem cell transplantation RESPIRATORY RESEARCH Englert, J. A., Cho, M. H., Lamb, A. E., Shumyatcher, M., Barragan-Bradford, D., Basil, M. C., Higuera, A., Isabelle, C., Vera, M., Dieffenbach, P. B., Fredenburgh, L. E., Kang, J. B., Bhatt, A. S., Antin, J. H., Ho, V. T., Soiffer, R. J., Howrylak, J. A., Himes, B. E., Baron, R. M. 2019; 20

  View details for DOI 10.1186/s12931-019-0981-6

  View details for Web of Science ID 000458078000001

• Surveying Gut Microbiome Research in Africans: Toward Improved Diversity and Representation. Trends in microbiology Brewster, R. n., Tamburini, F. B., Asiimwe, E. n., Oduaran, O. n., Hazelhurst, S. n., Bhatt, A. S. 2019

  Abstract

  Descriptive and translational investigations into the human gut microbiome (GM) are rapidly expanding; however, studies are largely restricted to industrialized populations in the USA and Europe. Little is known about microbial variability and its implications for health and disease in other parts of the world. Populations in Africa are particularly underrepresented. What limited research has been performed has focused on a few subject domains, including the impact of long-term lifestyle and dietary factors on GM ecology, its maturation during infancy, and the interrelationships between the microbiome, infectious disease, and undernutrition. Recently, international consortia have laid the groundwork for large-scale genomics and microbiome studies on the continent, with a particular interest in the epidemiologic transition to noncommunicable disease. Here, we survey the current landscape of GM scholarship in Africa and propose actionable recommendations to improve research capacity and output.

  View details for DOI 10.1016/j.tim.2019.05.006

  View details for PubMedID 31178123

• Evaluating Barriers and Opportunities in Delivering High-Quality Oncology Care in a Resource-Limited Setting Using a Comprehensive Needs Assessment Tool JOURNAL OF GLOBAL ONCOLOGY Nwachukwu, C. R., Mudasiru, O., Million, L., Sheth, S., Qamoos, H., Onah, J. O., Okemini, A., Rhodes, M., Barry, M., Banjo, A. A., Habeebu, M., Olasinde, T. A., Bhatt, A. S. 2018; 4

  View details for DOI 10.1200/JGO.18.00125

  View details for Web of Science ID 000462480700001

• Evaluating Barriers and Opportunities in Delivering High-Quality Oncology Care in a Resource-Limited Setting Using a Comprehensive Needs Assessment Tool. Journal of global oncology Nwachukwu, C. R., Mudasiru, O., Million, L., Sheth, S., Qamoos, H., Onah, J. O., Okemini, A., Rhodes, M., Barry, M., Banjo, A. A., Habeebu, M., Olasinde, T. A., Bhatt, A. S. 2018: 1–9

  Abstract

  PURPOSE: Despite recognition of both the growing cancer burden in low- and middle-income countries and the disproportionately high mortality rates in these settings, delivery of high-quality cancer care remains a challenge. The disparities in cancer care outcomes for many geographic regions result from barriers that are likely complex and understudied. This study describes the development and use of a streamlined needs assessment questionnaire (NAQ) to understand the barriers to providing quality cancer care, identifies areas for improvement, and formulates recommendations for implementation.METHODS: Using a comprehensive NAQ, in-depth interviews were conducted with 17 hospital staff involved in cancer care at two teaching hospitals in Nigeria. Data were analyzed using content analysis and organized into a framework with preset codes and emergent codes, where applicable.RESULTS: Data from the interviews were organized into six broad themes: staff, stuff, system, space, lack of palliative care, and provider bias, with key barriers within themes including: financial, infrastructural, lack of awareness, limited human capacity resources, lack of palliative care, and provider perspective on patient-related barriers to cancer care. Specific solutions based on ability to reasonably implement were subcategorized into short-, medium-, and long-term goals.CONCLUSION: This study provides a framework for a streamlined initial needs assessment and a unique discussion on the barriers to high-quality oncology care that are prevalent in resource-constrained settings. We report the feasibility of collecting and organizing data using a streamlined NAQ and provide a thorough and in-depth understanding of the challenges in this setting. Knowledge gained from the assessments will inform steps to improve oncology cancer in these settings.

  View details for PubMedID 30532992

• Read cloud sequencing elucidates microbiome dynamics in a hematopoietic cell transplant patient. Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Kang, J., Siranosian, B., Moss, E., Andermann, T., Bhatt, A. 2018; 2018: 234-241

  Abstract

  Low intestinal microbial diversity, often leading to domination of the intestine by a single organism, is associated with poor outcomes following hematopoietic cell transplantation (HCT). Understanding how certain organisms achieve domination in the intestine is limited by current metagenomic sequencing technologies, which are typically unable to reconstruct complete genome drafts without bacterial isolation and culture. Recently, we developed a metagenomic read cloud sequencing approach that provides significantly improved genome drafts for individual organisms compared to conventional short-read sequencing methods. Here, we apply read cloud sequencing to four longitudinal stool samples collected from an HCT patient before and after heavy antibiotic exposure. During this time period, the patient experienced Escherichia coli gut domination and an E. coli bloodstream infection. We find that read clouds enable the placement of multiple copies of antibiotic resistance genes both within and across genomes, and the presence of resistance genes correlates with the timing of antibiotics administered to the patient. Comparative genomic analysis reveals that the E. coli bloodstream infection likely originated from the gut. The pre-transplant E. coli genome harbors 46 known resistance genes, whereas all other organisms from the pre-transplant time point contain 5 or fewer resistance genes, supporting a model in which the E. coli outgrowth was a result of selection by heavy antibiotic exposure. This case study highlights the application of metagenomic read cloud sequencing in a clinical context to elucidate the genomic underpinnings of microbiome dynamics under extreme selective pressures.

  View details for DOI 10.1109/bibm.2018.8621297

  View details for PubMedID 33833903

  View details for PubMedCentralID PMC8026214

• Institutionalizing healthcare hackathons to promote diversity in collaboration in medicine. BMC medical education Wang, J. K., Roy, S. K., Barry, M., Chang, R. T., Bhatt, A. S. 2018; 18 (1): 269

  Abstract

  BACKGROUND: Medical students and healthcare professionals can benefit from exposure to cross-disciplinary teamwork and core concepts of medical innovation. Indeed, to address complex challenges in patient care, diversity in collaboration across medicine, engineering, business, and design is critical. However, a limited number of academic institutions have established cross-disciplinary opportunities for students and young professionals within these domains to work collaboratively towards diverse healthcare needs.METHODS: Drawing upon best practices from computer science and engineering, healthcare hackathons bring together interdisciplinary teams of students and professionals to collaborate, brainstorm, and build solutions to unmet clinical needs. Over the course of six months, a committee of 20 undergraduates, medical students, and physician advisors organized Stanford University's first healthcare hackathon (November 2016). Demographic data from initial applications were supplemented with responses from a post-hackathon survey gauging themes of diversity in collaboration, professional development, interest in medical innovation, and educational value. In designing and evaluating the event, the committee focused on measurable outcomes of diversity across participants (skillset, age, gender, academic degree), ideas (clinical needs), and innovations (projects).RESULTS: Demographic data (n=587 applicants, n=257 participants) reveal participants across diverse academic backgrounds, age groups, and domains of expertise were in attendance. From 50 clinical needs presented representing 19 academic fields, 40 teams ultimately formed and submitted projects spanning web (n=13) and mobile applications (n=13), artificial intelligence-based tools (n=6), and medical devices (n=3), among others. In post-hackathon survey responses (n=111), medical students and healthcare professionals alike noted a positive impact on their ability to work in multidisciplinary teams, learn from individuals of different backgrounds, and address complex healthcare challenges.CONCLUSIONS: Healthcare hackathons can encourage diversity across individuals, ideas, and projects to address clinical challenges. By providing an outline of Stanford's inaugural event, we hope more universities can adopt the healthcare hackathon model to promote diversity in collaboration in medicine.

  View details for PubMedID 30458759

• Institutionalizing healthcare hackathons to promote diversity in collaboration in medicine BMC MEDICAL EDUCATION Wang, J. K., Roy, S. K., Barry, M., Chang, R. T., Bhatt, A. S. 2018; 18

  View details for DOI 10.1186/s12909-018-1385-x

  View details for Web of Science ID 000450779900001

• Persistence of endothelial thrombomodulin in a patient with infectious purpura fulminans treated with protein C concentrate. Blood advances Bendapudi, P. K., Robbins, A., LeBoeuf, N., Pozdnyakova, O., Bhatt, A., Duke, F., Sells, R., McQuiston, J., Humrighouse, B., Rouaisnel, B., Colling, M., Stephenson, K. E., Saavedra, A., Losman, J. 2018; 2 (21): 2917–21

  View details for PubMedID 30396911

• Persistence of endothelial thrombomodulin in a patient with infectious purpura fulminans treated with protein C concentrate BLOOD ADVANCES Bendapudi, P. K., Robbins, A., LeBoeuf, N., Pozdnyakova, O., Bhatt, A., Duke, F., Sells, R., McQuiston, J., Humrighouse, B., Rouaisnel, B., Colling, M., Stephenson, K. E., Saavedra, A., Losman, J. 2018; 2 (21): 2917–21

  View details for DOI 10.1182/bloodadvances.2018024430

  View details for Web of Science ID 000450684800011

• Antibiotic practice patterns in hematopoietic cell transplantation: A survey of blood and marrow transplant clinical trials network centers AMERICAN JOURNAL OF HEMATOLOGY Rashidi, A., Wangjam, T., Bhatt, A. S., Weisdorf, D. J., Holtan, S. G., BMT CTN Investigators 2018; 93 (11): E348–E350

  View details for PubMedID 30058189

  View details for PubMedCentralID PMC6196101

• High-quality genome sequences of uncultured microbes by assembly of read clouds NATURE BIOTECHNOLOGY Bishara, A., Moss, E. L., Kolmogorov, M., Parada, A. E., Weng, Z., Sidow, A., Dekas, A. E., Batzoglou, S., Bhatt, A. S. 2018; 36 (11): 1067-+

  View details for DOI 10.1038/nbt.4266

  View details for Web of Science ID 000450374000020

• Diversity of resistance mechanisms in carbapenem-resistant Enterobacteriaceae at a health care system in Northern California, from 2013 to 2016. Diagnostic microbiology and infectious disease Senchyna, F., Gaur, R. L., Sandlund, J., Truong, C., Tremintin, G., Kultz, D., Gomez, C. A., Tamburini, F. B., Andermann, T., Bhatt, A., Tickler, I., Watz, N., Budvytiene, I., Shi, G., Tenover, F. C., Banaei, N. 2018

  Abstract

  The mechanism of resistance in carbapenem-resistant Enterobacteriaceae (CRE) has therapeutic implications. We comprehensively characterized emerging mechanisms of resistance in CRE between 2013 and 2016 at a health system in Northern California. A total of 38.7% (24/62) of CRE isolates were carbapenemase gene-positive, comprising 25.0% (6/24) blaOXA-48 like, 20.8% (5/24) blaKPC, 20.8% (5/24) blaNDM, 20.8% (5/24) blaSME, 8.3% (2/24) blaIMP, and 4.2% (1/24) blaVIM. Between carbapenemases and porin loss, the resistance mechanism was identified in 95.2% (59/62) of CRE isolates. Isolates expressing blaKPC were 100% susceptible to ceftazidime-avibactam, meropenem-vaborbactam, and imipenem-relebactam; blaOXA-48 like-positive isolates were 100% susceptible to ceftazidime-avibactam; and metallo beta-lactamase-positive isolates were nearly all nonsusceptible to above antibiotics. Carbapenemase gene-negative CRE were 100% (38/38), 92.1% (35/38), 89.5% (34/38), and 31.6% (12/38) susceptible to ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, and ceftolozane-tazobactam, respectively. None of the CRE strains were identical by whole genome sequencing. At this health system, CRE were mediated by diverse mechanisms with predictable susceptibility to newer beta-lactamase inhibitors.

  View details for PubMedID 30482638

• Data mining of digitized health records in a resource-constrained setting reveals that timely immunophenotyping is associated with improved breast cancer outcomes. BMC cancer Lopez-Pineda, A., Rodriguez-Moran, M. F., Alvarez-Aguilar, C., Fuentes Valle, S. M., Acosta-Rosales, R., Bhatt, A. S., Sheth, S. N., Bustamante, C. D. 2018; 18 (1): 933

  Abstract

  BACKGROUND: Organizations that issue guidance on breast cancer recommend the use of immunohistochemistry (IHC) for providing appropriate and precise care. However, little focus has been directed to the identification of maximum allowable turnaround times for IHC, which is necessary given the diversity of hospital settings in the world. Much less effort has been committed to the development of digital tools that allow hospital administrators to monitor service utilization histories of their patients.METHODS: In this retrospective cohort study, we reviewed electronic and paper medical records of all suspected breast cancer patients treated at one secondary-care hospital of the Mexican Institute of Social Security (IMSS), located in western Mexico. We then followed three years of medical history of those patients with IHC testing.RESULTS: In 2014, there were 402 breast cancer patients, of which 30 (7.4% of total) were tested for some IHC biomarker (ER, PR, HER2). The subtyping allowed doctors to adjust (56.7%) or confirm (43.3%) the initial therapeutic regimen. The average turnaround time was 56days. Opportune IHC testing was found to be beneficial when it was available before or during the first rounds of chemotherapy.CONCLUSIONS: The use of data mining tools applied to health record data revealed that there is an association between timely immunohistochemistry and improved outcomes in breast cancer patients. Based on this finding, inclusion of turnaround time in clinical guidelines is recommended. As much of the health data in the country becomes digitized, our visualization tools allow a digital dashboard of the hospital service utilization histories.

  View details for PubMedID 30261931

• Data mining of digitized health records in a resource-constrained setting reveals that timely immunophenotyping is associated with improved breast cancer outcomes BMC CANCER Lopez-Pineda, A., Rodriguez-Moran, M. F., Alvarez-Aguilar, C., Fuentes Valle, S. M., Acosta-Rosales, R., Bhatt, A. S., Sheth, S. N., Bustamante, C. D. 2018; 18

  View details for DOI 10.1186/s12885-018-4833-4

  View details for Web of Science ID 000445959100003

• Digesting New Developments in Biosensors NEW ENGLAND JOURNAL OF MEDICINE Bhatt, A. S. 2018; 379 (7): 686–88

  View details for DOI 10.1056/NEJMcibr1806952

  View details for Web of Science ID 000441659100015

• A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection CELL HOST & MICROBE Jacobson, A., Lam, L., Rajendram, M., Tamburini, F., Honeycutt, J., Trung Pham, Van Treuren, W., Pruss, K., Stabler, S., Lugo, K., Bouley, D. M., Vilches-Moure, J. G., Smith, M., Sonnenburg, J. L., Bhatt, A. S., Huang, K., Monack, D. 2018; 24 (2): 296-+

  View details for DOI 10.1016/j.chom.2018.07.002

  View details for Web of Science ID 000441083900016

• A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection. Cell host & microbe Jacobson, A., Lam, L., Rajendram, M., Tamburini, F., Honeycutt, J., Pham, T., Van Treuren, W., Pruss, K., Stabler, S. R., Lugo, K., Bouley, D. M., Vilches-Moure, J. G., Smith, M., Sonnenburg, J. L., Bhatt, A. S., Huang, K. C., Monack, D. 2018

  Abstract

  The intestinal microbiota provides colonization resistance against pathogens, limiting pathogen expansion and transmission. These microbiota-mediated mechanisms were previously identified by observing loss of colonization resistance after antibiotic treatment or dietary changes, which severely disrupt microbiota communities. We identify a microbiota-mediated mechanism of colonization resistance against Salmonella enterica serovar Typhimurium (S. Typhimurium) by comparing high-complexity commensal communities with different levels of colonization resistance. Using inbred mouse strains with different infection dynamics and S. Typhimurium intestinal burdens, we demonstrate that Bacteroides species mediate colonization resistance against S. Typhimurium by producing the short-chain fatty acid propionate. Propionate directly inhibits pathogen growth invitro by disrupting intracellular pH homeostasis, and chemically increasing intestinal propionate levels protects mice from S.Typhimurium. In addition, administering susceptible mice Bacteroides, but not a propionate-production mutant, confers resistance to S. Typhimurium. This work provides mechanistic understanding into the role of individualized microbial communities in host-to-host variability of pathogen transmission.

  View details for PubMedID 30057174

• The Microbiome and Hematopoietic Cell Transplantation: Past, Present, and Future BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION Andermann, T. M., Peled, J. U., Ho, C., Reddy, P., Riches, M., Storb, R., Teshima, T., van den Brink, M. M., Alousi, A., Balderman, S., Chiusolo, P., Clark, W. B., Holler, E., Howard, A., Kean, L. S., Koh, A. Y., McCarthy, P. L., McCarty, J. M., Mohty, M., Nakamura, R., Rezvani, K., Segal, B. H., Shaw, B. E., Shpall, E. J., Sung, A. D., Weber, D., Whangbo, J., Wingard, J. R., Wood, W. A., Perales, M., Jenq, R. R., Bhatt, A. S., Blood Marrow Transplant Clinical 2018; 24 (7): 1322–40

  View details for DOI 10.1016/j.bbmt.2018.02.009

  View details for Web of Science ID 000440879800004

• Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota. Cell Tropini, C., Moss, E. L., Merrill, B. D., Ng, K. M., Higginbottom, S. K., Casavant, E. P., Gonzalez, C. G., Fremin, B., Bouley, D. M., Elias, J. E., Bhatt, A. S., Huang, K. C., Sonnenburg, J. L. 2018; 173 (7): 1742

  Abstract

  Osmotic diarrhea is a prevalent condition in humans caused by food intolerance, malabsorption, and widespread laxative use. Here, we assess the resilience of the gut ecosystem to osmotic perturbation at multiple length and timescales using mice as model hosts. Osmotic stress caused reproducible extinction of highly abundant taxa and expansion of less prevalent members in human and mouse microbiotas. Quantitative imaging revealed decimation of the mucus barrier during osmotic perturbation, followed by recovery. The immune system exhibited temporary changes in cytokine levels and a lasting IgG response against commensal bacteria. Increased osmolality prevented growth of commensal strains invitro, revealing one mechanism contributing to extinction. Environmental availability of microbiota members mitigated extinction events, demonstrating how species reintroduction can affect community resilience. Our findings (1) demonstrate that even mild osmotic diarrhea can cause lasting changes to the microbiota and host and (2) lay the foundation for interventions that increase system-wide resilience.

  View details for PubMedID 29906449

• Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota CELL Tropini, C., Moss, E., Merrill, B., Ng, K., Higginbottom, S., Casavant, E., Gonzalez, C., Fremin, B., Bouley, D., Elias, J., Bhatt, A., Huang, K., Sonnenburg, J. 2018; 173 (7): 1742-+

  View details for DOI 10.1016/j.cell.2018.05.008

  View details for Web of Science ID 000437004000021

• AGBT meeting report GENOME BIOLOGY Bhatt, A. S., Curtis, C. 2018; 19: 60

  Abstract

  The Annual Advances in Genome Biology and Technology (AGBT) General Meeting was held in Orlando, Florida, USA, on the 12-15 February 2018. Professors Ami S. Bhatt and Christina Curtis from Stanford University, USA, report advances and applications in the field that were discussed at the meeting.

  View details for PubMedID 29784033

• The Microbiome and Hematopoietic Cell Transplantation: Past, Present, and Future. Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation Andermann, T. M., Peled, J. U., Ho, C., Reddy, P., Riches, M., Storb, R., Teshima, T., van den Brink, M. R., Alousi, A., Balderman, S., Chiusolo, P., Clark, W. B., Holler, E., Howard, A., Kean, L. S., Koh, A. Y., McCarthy, P. L., McCarty, J. M., Mohty, M., Nakamura, R., Rezvani, K., Segal, B. H., Shaw, B. E., Shpall, E. J., Sung, A. D., Weber, D., Whangbo, J., Wingard, J. R., Wood, W. A., Perales, M., Jenq, R. R., Bhatt, A. S., Blood and Marrow Transplant Clinical Trials Network 2018

  View details for PubMedID 29471034

• In Translation: With probiotics, resistance is not always futile Cell Host & Microbe Severyn, C. J., Bhatt, A. S. 2018; 24: 334-336

  View details for DOI 10.1016/j.chom.2018.08.014

• With Probiotics, Resistance Is Not Always Futile. Cell host & microbe Severyn, C. J., Bhatt, A. S. 2018; 24 (3): 334–36

  Abstract

  Probiotics and other bacteriotherapies are actively being explored and applied as symptom- and disease-modifying agents. In a recent issue of Cell, two papers contribute to our understanding of how live bacterial therapies variably affect individuals and the short- and longer-term impact of these therapies on colonization and host response.

  View details for PubMedID 30212646

• Read cloud sequencing elucidates microbiome dynamics in a hematopoietic cell transplant patient Kang, J., Siranosian, B., Moss, E., Andermann, T., Bhatt, A., Zheng, H., Callejas, Z., Griol, D., Wang, H., Hu, Schmidt, H., Baumbach, J., Dickerson, J., Zhang, L. IEEE. 2018: 234–41

  View details for Web of Science ID 000458654000043

• Household triclosan and triclocarban effects on the infant and maternal microbiome EMBO MOLECULAR MEDICINE Ribado, J. V., Ley, C., Haggerty, T. D., Tkachenko, E., Bhatt, A. S., Parsonnet, J. 2017; 9 (12): 1732–41

  View details for DOI 10.15252/emmm.201707882

  View details for Web of Science ID 000416867700009

• Allied Commensal Forces against Vancomycin-Resistant Enterococci CELL HOST & MICROBE Fremin, B. J., Bhatt, A. S. 2017; 21 (5): 559–60

  Abstract

  In this issue of Cell Host & Microbe, Caballero et al. (2017) define a precise, limited consortium of commensal bacteria that restores resistance to colonization by clinically vexing vancomycin-resistant Enterococcus species.

  View details for PubMedID 28494236

  View details for PubMedCentralID PMC5603308

• Quantitative Computed Tomography Assessment of Bronchiolitis Obliterans Syndrome after Lung Transplantation. Clinical transplantation Gazourian, L., Ash, S., Meserve, E. E., Diaz, A., Estepar, R. S., El-Chemaly, S. Y., Rosas, I. O., Divo, M., Fuhlbrigge, A. L., Camp, P. C., Ho, V. T., Bhatt, A. S., Goldberg, H. J., Sholl, L. M., Washko, G. R. 2017

  Abstract

  Bronchiolitis obliterans syndrome (BOS) is a clinical manifestation of chronic allograft rejection following lung transplantation. We examined the quantitative measurements of the proximal airway and vessels and pathologic correlations in subjects with BOS.Patients who received a lung transplant at the Brigham and Women's Hospital between December 1, 2002 and December 31, 2010 were included in this study. We characterized the quantitative CT measures of proximal airways and vessels and pathological changes.Ninety-four (46.1%) of the 204 subjects were included in the study. There was a significant increase in the airway vessel ratio in subjects who developed progressive BOS compared to controls and non-progressors. There was a significant increase in airway lumen area and decrease in vessel cross-sectional area in patients with BOS compared to controls. Patients with BOS had a significant increase in proximal airway fibrosis compared to controls.BOS is characterized by central airway dilation and vascular remodeling, the degree of which is correlated to decrements in lung function. Our data suggest that progressive BOS is a pathologic process that affects both the central and distal airways.

  View details for DOI 10.1111/ctr.12943

  View details for PubMedID 28244139

• Technological solutions for global hematology and oncology BLOOD ADVANCES Bhatt, A. S. 2017; 1 (6): 396

  View details for PubMedID 29296953

• Antibiotic-mediated modification of the intestinal microbiome in allogeneic hematopoietic stem cell transplantation BONE MARROW TRANSPLANTATION Whangbo, J., Ritz, J., Bhatt, A. 2017; 52 (2): 183-190

  Abstract

  Allogeneic hematopoietic stem cell transplantation (HSCT) is curative for many patients with severe benign and malignant hematologic disorders. The success of allogeneic HSCT is limited by the development of transplant-related complications such as acute graft-versus-host disease (GvHD). Early pre-clinical studies suggested that intestinal microflora contribute to the pathogenesis of acute GvHD, and that growth suppression or eradication of intestinal bacteria prevented the development of acute GvHD even in MHC-mismatched transplants. These observations led to the practice of gut decontamination (GD) with oral non-absorbable antibiotics in patients undergoing allogeneic HSCT as a method of acute GvHD prophylaxis. Microbiome studies in the modern sequencing era are beginning to challenge the benefit of this practice. In this review, we provide a historical perspective on the practice of GD and highlight findings from the limited number of clinical trials evaluating the use of GD for acute GvHD prevention in allogeneic HSCT patients. In addition, we examine the role of the gut microbiota in allogeneic HSCT in the context of recent studies linking the microflora to regulation of intestinal immune homeostasis. We discuss the implications of these findings for future strategies to reduce acute GvHD risk by selective manipulation of the microbiota.Bone Marrow Transplantation advance online publication, 15 August 2016; doi:10.1038/bmt.2016.206.

  View details for DOI 10.1038/bmt.2016.206

  View details for Web of Science ID 000394134300003

• Microbes prevent HSPCs from "NOD"-ing off. Blood Bhatt, A. S. 2017; 129 (2): 139-140

  View details for DOI 10.1182/blood-2016-11-750562

  View details for PubMedID 28082290

• Household triclosan and triclocarban effects on the infant and maternal microbiome. EMBO molecular medicine Ribado, J. V., Ley, C. n., Haggerty, T. D., Tkachenko, E. n., Bhatt, A. S., Parsonnet, J. n. 2017; 9 (12): 1732–41

  Abstract

  In 2016, the US Food and Drug Administration banned the use of specific microbicides in some household and personal wash products due to concerns that these chemicals might induce antibiotic resistance or disrupt human microbial communities. Triclosan and triclocarban (referred to as TCs) are the most common antimicrobials in household and personal care products, but the extent to which TC exposure perturbs microbial communities in humans, particularly during infant development, was unknown. We conducted a randomized intervention of TC-containing household and personal care products during the first year following birth to characterize whether TC exposure from wash products perturbs microbial communities in mothers and their infants. Longitudinal survey of the gut microbiota using 16S ribosomal RNA amplicon sequencing showed that TC exposure from wash products did not induce global reconstruction or loss of microbial diversity of either infant or maternal gut microbiotas. Broadly antibiotic-resistant species from the phylum Proteobacteria, however, were enriched in stool samples from mothers in TC households after the introduction of triclosan-containing toothpaste. When compared by urinary triclosan level, agnostic to treatment arm, infants with higher triclosan levels also showed an enrichment of Proteobacteria species. Despite the minimal effects of TC exposure from wash products on the gut microbial community of infants and adults, detected taxonomic differences highlight the need for consumer safety testing of antimicrobial self-care products on the human microbiome and on antibiotic resistance.

  View details for PubMedID 29030459

• Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients. PloS one Moss, E. L., Falconer, S. B., Tkachenko, E. n., Wang, M. n., Systrom, H. n., Mahabamunuge, J. n., Relman, D. A., Hohmann, E. L., Bhatt, A. S. 2017; 12 (8): e0182585

  Abstract

  Immunocompromised individuals are at high risk of developing Clostridium difficile-associated disease (CDAD). Fecal microbiota transplantation (FMT) is a highly effective therapy for refractory or recurrent CDAD and, despite safety concerns, has recently been offered to immunocompromised patients. We investigated the genomics of bacterial composition following FMT in immunocompromised patients over a 1-year period. Metagenomic, strain and gene-level bacterial dynamics were characterized in two CDAD-affected hematopoietic stem cell (HCT) recipients following FMT. We found alterations in gene content, including loss of virulence and antibiotic resistance genes. These alterations were accompanied by long-term bacterial divergence at the species and strain levels. Our findings suggest limited durability of the specific bacterial consortium introduced with FMT and indicate that alterations of the functional potential of the microbiome are more complex than can be inferred by taxonomic information alone. Our observation that FMT alone cannot induce long-term donor-like alterations of the microbiota of HCT recipients suggests that FMT cannot indefinitely supersede environmental and/or host factors in shaping bacterial composition.

  View details for PubMedID 28827811

• The Burden of Cancer in Asian Americans: A Report of National Mortality Trends by Asian Ethnicity CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Thompson, C. A., Gomez, S. L., Hastings, K. G., Kapphahn, K., Yu, P., Shariff-Marco, S., Bhatt, A. S., Wakelee, H. A., Patel, M. I., Cullen, M. R., Palaniappan, L. P. 2016; 25 (10): 1371-1382

  Abstract

  Asian Americans (AA) are the fastest growing U.S. population, and when properly distinguished by their ethnic origins, exhibit substantial heterogeneity in socioeconomic status, health behaviors, and health outcomes. Cancer is the second leading cause of death in the United States, yet trends and current patterns in the mortality burden of cancer among AA ethnic groups have not been documented.We report age-adjusted rates, standardized mortality ratios, and modeled trends in cancer-related mortality in the following AA ethnicities: Asian Indians, Chinese, Filipinos, Japanese, Koreans, and Vietnamese, from 2003 to 2011, with non-Hispanic whites (NHW) as the reference population.For most cancer sites, AAs had lower cancer mortality than NHWs; however, mortality patterns were heterogeneous across AA ethnicities. Stomach and liver cancer mortality was very high, particularly among Chinese, Koreans, and Vietnamese, for whom these two cancer types combined accounted for 15% to 25% of cancer deaths, but less than 5% of cancer deaths in NHWs. In AA women, lung cancer was a leading cause of death, but (unlike males and NHW females) rates did not decline over the study period.Ethnicity-specific analyses are critical to understanding the national burden of cancer among the heterogeneous AA population.Our findings highlight the need for disaggregated reporting of cancer statistics in AAs and warrant consideration of tailored screening programs for liver and gastric cancers. Cancer Epidemiol Biomarkers Prev; 25(10); 1371-82. ©2016 AACR.

  View details for DOI 10.1158/1055-9965.EPI-16-0167

  View details for PubMedID 27694108

• Infection Rates among Acute Leukemia Patients Receiving Alternative Donor Hematopoietic Cell Transplantation. Biology of blood and marrow transplantation Ballen, K., Woo Ahn, K., Chen, M., Abdel-Azim, H., Ahmed, I., Aljurf, M., Antin, J., Bhatt, A. S., Boeckh, M., Chen, G., Dandoy, C., George, B., Laughlin, M. J., Lazarus, H. M., MacMillan, M. L., Margolis, D. A., Marks, D. I., Norkin, M., Rosenthal, J., Saad, A., Savani, B., Schouten, H. C., Storek, J., Szabolcs, P., Ustun, C., Verneris, M. R., Waller, E. K., Weisdorf, D. J., Williams, K. M., Wingard, J. R., Wirk, B., Wolfs, T., Young, J. H., Auletta, J., Komanduri, K. V., Lindemans, C., Riches, M. L. 2016; 22 (9): 1636-1645

  Abstract

  Alternative graft sources (umbilical cord blood [UCB], matched unrelated donors [MUD], or mismatched unrelated donors [MMUD]) enable patients without a matched sibling donor to receive potentially curative hematopoietic cell transplantation (HCT). Retrospective studies demonstrate comparable outcomes among different graft sources. However, the risk and types of infections have not been compared among graft sources. Such information may influence the choice of a particular graft source. We compared the incidence of bacterial, viral, and fungal infections in 1781 adults with acute leukemia who received alternative donor HCT (UCB, n= 568; MUD, n = 930; MMUD, n = 283) between 2008 and 2011. The incidences of bacterial infection at 1 year were 72%, 59%, and 65% (P < .0001) for UCB, MUD, and MMUD, respectively. Incidences of viral infection at 1 year were 68%, 45%, and 53% (P < .0001) for UCB, MUD, and MMUD, respectively. In multivariable analysis, bacterial, fungal, and viral infections were more common after either UCB or MMUD than after MUD (P < .0001). Bacterial and viral but not fungal infections were more common after UCB than MMUD (P = .0009 and <.0001, respectively). The presence of viral infection was not associated with an increased mortality. Overall survival (OS) was comparable among UCB and MMUD patients with Karnofsky performance status (KPS) ≥ 90% but was inferior for UCB for patients with KPS < 90%. Bacterial and fungal infections were associated with poorer OS. Future strategies focusing on infection prevention and treatment are indicated to improve HCT outcomes.

  View details for DOI 10.1016/j.bbmt.2016.06.012

  View details for PubMedID 27343716

• Antibiotics in Hematopoietic Cell Transplantation: Adversaries or Allies? BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION Andermann, T. M., Bhatt, A. S. 2016; 22 (6): 972-974

  View details for DOI 10.1016/j.bbmt.2016.04.002

  View details for PubMedID 27095689

• Mapping global cancer research and control in areas of low and middle income: The need for shared data on a single, interactive platform Chisti, A., Sharara, N., Gupta, M., Rosenberg, I., Abudu, R., Morgan, C., Duncan, K., Silkensen, S., Craycroft, J., Silva, J., Andre, B., Trimble, E., Bhatt, A., Huang, F. W. AMER SOC CLINICAL ONCOLOGY. 2016

  View details for DOI 10.1200/JCO.2016.34.15_suppl.e18048

  View details for Web of Science ID 000404711503193

• Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice SCIENCE TRANSLATIONAL MEDICINE Shono, Y., Docampo, M. D., Peled, J. U., Perobelli, S. M., Velardi, E., Tsai, J. J., Slingerland, A. E., Smith, O. M., Young, L. F., Gupta, J., Lieberman, S. R., Jay, H. V., Ahr, K. F., Rodriguez, K. A., Xu, K., Calarfiore, M., Poeck, H., Caballero, S., Devlin, S. M., Rapaport, F., Dudakov, J. A., Hanash, A. M., Gyurkocza, B., Murphy, G. F., Gomes, C., Liu, C., Moss, E. L., Falconer, S. B., Bhatt, A. S., Taur, Y., Pamer, E. G., van den Brink, M. R., Jenq, R. R. 2016; 8 (339)

  Abstract

  Intestinal bacteria may modulate the risk of infection and graft-versus-host disease (GVHD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Allo-HSCT recipients often develop neutropenic fever, which is treated with antibiotics that may target anaerobic bacteria in the gut. We retrospectively examined 857 allo-HSCT recipients and found that treatment of neutropenic fever with imipenem-cilastatin and piperacillin-tazobactam antibiotics was associated with increased GVHD-related mortality at 5 years (21.5% for imipenem-cilastatin-treated patients versus 13.1% for untreated patients, P = 0.025; 19.8% for piperacillin-tazobactam-treated patients versus 11.9% for untreated patients, P = 0.007). However, two other antibiotics also used to treat neutropenic fever, aztreonam and cefepime, were not associated with GVHD-related mortality (P = 0.78 and P = 0.98, respectively). Analysis of stool specimens from allo-HSCT recipients showed that piperacillin-tazobactam administration was associated with perturbation of gut microbial composition. Studies in mice demonstrated aggravated GVHD mortality with imipenem-cilastatin or piperacillin-tazobactam compared to aztreonam (P < 0.01 and P < 0.05, respectively). We found pathological evidence for increased GVHD in the colon of imipenem-cilastatin-treated mice (P < 0.05), but no difference in the concentration of short-chain fatty acids or numbers of regulatory T cells. Notably, imipenem-cilastatin treatment of mice with GVHD led to loss of the protective mucus lining of the colon (P < 0.01) and the compromising of intestinal barrier function (P < 0.05). Sequencing of mouse stool specimens showed an increase in Akkermansia muciniphila (P < 0.001), a commensal bacterium with mucus-degrading capabilities, raising the possibility that mucus degradation may contribute to murine GVHD. We demonstrate an underappreciated risk for the treatment of allo-HSCT recipients with antibiotics that may exacerbate GVHD in the colon.

  View details for DOI 10.1126/scitranslmed.aaf2311

  View details for PubMedID 27194729

• Fecal Microbiota Transplant Is a Potentially Safe and Effective Treatment for Clostridium Difficile Infection in Hematopoietic Stem Cell Recipients Falconer, S., Moss, E., Andermann, T., Systrom, H., Mahabamunuge, J., Hohmann, E., Bhatt, A. S. ELSEVIER SCIENCE INC. 2016: S53–S54

  View details for DOI 10.1016/j.bbmt.2015.11.340

  View details for Web of Science ID 000370910300050

• Microbiota Manipulation With Prebiotics and Probiotics in Patients Undergoing Stem Cell Transplantation CURRENT HEMATOLOGIC MALIGNANCY REPORTS Andermann, T. M., Rezvani, A., Bhatt, A. S. 2016; 11 (1): 19-28

  Abstract

  Hematopoietic stem cell transplantation (HSCT) is a potentially life-saving therapy that often comes at the cost of complications such as graft-versus-host disease and post-transplant infections. With improved technology to understand the ecosystem of microorganisms (viruses, bacteria, fungi, and microeukaryotes) that make up the gut microbiota, there is increasing evidence of the microbiota's contribution to the development of post-transplant complications. Antibiotics have traditionally been the mainstay of microbiota-altering therapies available to physicians. Recently, interest is increasing in the use of prebiotics and probiotics to support the development and sustainability of a healthier microbiota. In this review, we will describe the evidence for the use of prebiotics and probiotics in combating microbiota dysbiosis and explore the ways in which they may be used in future research to potentially improve clinical outcomes and decrease rates of graft-versus-host disease (GVHD) and post-transplant infection.

  View details for DOI 10.1007/s11899-016-0302-9

  View details for Web of Science ID 000372595100004

• Microbiota Manipulation With Prebiotics and Probiotics in Patients Undergoing Stem Cell Transplantation. Current hematologic malignancy reports Andermann, T. M., Rezvani, A., Bhatt, A. S. 2016

  Abstract

  Hematopoietic stem cell transplantation (HSCT) is a potentially life-saving therapy that often comes at the cost of complications such as graft-versus-host disease and post-transplant infections. With improved technology to understand the ecosystem of microorganisms (viruses, bacteria, fungi, and microeukaryotes) that make up the gut microbiota, there is increasing evidence of the microbiota's contribution to the development of post-transplant complications. Antibiotics have traditionally been the mainstay of microbiota-altering therapies available to physicians. Recently, interest is increasing in the use of prebiotics and probiotics to support the development and sustainability of a healthier microbiota. In this review, we will describe the evidence for the use of prebiotics and probiotics in combating microbiota dysbiosis and explore the ways in which they may be used in future research to potentially improve clinical outcomes and decrease rates of graft-versus-host disease (GVHD) and post-transplant infection.

  View details for DOI 10.1007/s11899-016-0302-9

  View details for PubMedID 26780719

• Complete hematologic response of early T-cell progenitor acute lymphoblastic leukemia to the ?-secretase inhibitor BMS-906024: genetic and epigenetic findings in an outlier case. Cold Spring Harbor molecular case studies Knoechel, B., Bhatt, A., Pan, L., Pedamallu, C. S., Severson, E., Gutierrez, A., Dorfman, D. M., Kuo, F. C., Kluk, M., Kung, A. L., Zweidler-McKay, P., Meyerson, M., Blacklow, S. C., DeAngelo, D. J., Aster, J. C. 2015; 1 (1)

  Abstract

  Notch pathway antagonists such as γ-secretase inhibitors (GSIs) are being tested in diverse cancers, but exceptional responses have yet to be reported. We describe the case of a patient with relapsed/refractory early T-cell progenitor acute lymphoblastic leukemia (ETP-ALL) who achieved a complete hematologic response following treatment with the GSI BMS-906024. Whole-exome sequencing of leukemic blasts revealed heterozygous gain-of-function driver mutations in NOTCH1, CSF3R, and PTPN11, and a homozygous/hemizygous loss-of-function mutation in DNMT3A. The three gain-of-function mutations were absent from remission marrow cells, but the DNMT3A mutation persisted in heterozygous form in remission marrow, consistent with an origin for the patient's ETP-ALL from clonal hematopoiesis. Ex vivo culture of ETP-ALL blasts confirmed high levels of activated NOTCH1 that were repressed by GSI treatment, and RNA-seq documented that GSIs downregulated multiple known Notch target genes. Surprisingly, one potential target gene that was unaffected by GSIs was MYC, a key Notch target in GSI-sensitive T-ALL of cortical T-cell type. H3K27ac super-enhancer landscapes near MYC showed a pattern previously reported in acute myeloid leukemia (AML) that is sensitive to BRD4 inhibitors, and in line with this ETP-ALL blasts downregulated MYC in response to the BRD4 inhibitor JQ1. To our knowledge, this is the first example of complete response of a Notch-mutated ETP-ALL to a Notch antagonist and is also the first description of chromatin landscapes associated with ETP-ALL. Our experience suggests that additional attempts to target Notch in Notch-mutated ETP-ALL are merited.

  View details for DOI 10.1101/mcs.a000539

  View details for PubMedID 27148573

• Launching an Interactive Cancer Projects Map: A Collaborative Approach to Global Cancer Research and Program Development. Journal of global oncology Trimble, E. L., Chisti, A. A., Craycroft, J. A., Duncan, K., Gupta, M., Gutierrez, D., Rosenberg, I., Sharara, N., Sivaram, S., Topazian, H. M., Wang, J. J., Williams, M. J., Huang, F. W., Bhatt, A. S. 2015; 1 (1): 7–10

  View details for PubMedID 28804766

• Epidemiologic Investigation of a Cluster of Neuroinvasive Bacillus cereus Infections in 5 Patients With Acute Myelogenous Leukemia. Open forum infectious diseases Rhee, C., Klompas, M., Tamburini, F. B., Fremin, B. J., Chea, N., Epstein, L., Halpin, A. L., Guh, A., Gallen, R., Coulliette, A., Gee, J., Hsieh, C., Desjardins, C. A., Pedamullu, C. S., DeAngelo, D. J., Manzo, V. E., Folkerth, R. D., Milner, D. A., Pecora, N., Osborne, M., Chalifoux-Judge, D., Bhatt, A. S., Yokoe, D. S. 2015; 2 (3): ofv096-?

  Abstract

  Background.  Five neuroinvasive Bacillus cereus infections (4 fatal) occurred in hospitalized patients with acute myelogenous leukemia (AML) during a 9-month period, prompting an investigation by infection control and public health officials. Methods.  Medical records of case-patients were reviewed and a matched case-control study was performed. Infection control practices were observed. Multiple environmental, food, and medication samples common to AML patients were cultured. Multilocus sequence typing was performed for case and environmental B cereus isolates. Results.  All 5 case-patients received chemotherapy and had early-onset neutropenic fevers that resolved with empiric antibiotics. Fever recurred at a median of 17 days (range, 9-20) with headaches and abrupt neurological deterioration. Case-patients had B cereus identified in central nervous system (CNS) samples by (1) polymerase chain reaction or culture or (2) bacilli seen on CNS pathology stains with high-grade B cereus bacteremia. Two case-patients also had colonic ulcers with abundant bacilli on autopsy. No infection control breaches were observed. On case-control analysis, bananas were the only significant exposure shared by all 5 case-patients (odds ratio, 9.3; P = .04). Five environmental or food isolates tested positive for B cereus, including a homogenized banana peel isolate and the shelf of a kitchen cart where bananas were stored. Multilocus sequence typing confirmed that all case and environmental strains were genetically distinct. Multilocus sequence typing-based phylogenetic analysis revealed that the organisms clustered in 2 separate clades. Conclusions.  The investigation of this neuroinvasive B cereus cluster did not identify a single point source but was suggestive of a possible dietary exposure. Our experience underscores the potential virulence of B cereus in immunocompromised hosts.

  View details for DOI 10.1093/ofid/ofv096

  View details for PubMedID 26269794

• The human microbiome in hematopoiesis and hematologic disorders. Blood Manzo, V. E., Bhatt, A. S. 2015; 126 (3): 311-318

  Abstract

  Humans are now understood to be in complex symbiosis with a diverse ecosystem of microbial organisms, including bacteria, viruses, and fungi. Efforts to characterize the role of these microorganisms, commonly referred as the microbiota, in human health have sought to answer the fundamental questions of what organisms are present, how are they functioning to interact with human cells, and by what mechanism are these interactions occurring. In this review, we describe recent efforts to describe the microbiota in healthy and diseased individuals, summarize the role of various molecular technologies (ranging from 16S ribosomal RNA to shotgun metagenomic sequencing) in enumerating the community structure of the microbiota, and explore known interactions between the microbiota and humans, with a focus on the microbiota's role in hematopoiesis and hematologic diseases.

  View details for DOI 10.1182/blood-2015-04-574392

  View details for PubMedID 26012569

• DNA copy number analysis of metastatic urothelial carcinoma with comparison to primary tumors BMC CANCER Bambury, R. M., Bhatt, A. S., Riester, M., Pedamallu, C. S., Duke, F., Bellmunt, J., Stack, E. C., Werner, L., Park, R., Iyer, G., Loda, M., Kantoff, P. W., Michor, F., Meyerson, M., Rosenberg, J. E. 2015; 15

  Abstract

  To date, there have been no reports characterizing the genome-wide somatic DNA chromosomal copy-number alteration landscape in metastatic urothelial carcinoma. We sought to characterize the DNA copy-number profile in a cohort of metastatic samples and compare them to a cohort of primary urothelial carcinoma samples in order to identify changes that are associated with progression from primary to metastatic disease.Using molecular inversion probe array analysis we compared genome-wide chromosomal copy-number alterations between 30 metastatic and 29 primary UC samples. Whole transcriptome RNA-Seq analysis was also performed in primary and matched metastatic samples which was available for 9 patients.Based on a focused analysis of 32 genes in which alterations may be clinically actionable, there were significantly more amplifications/deletions in metastases (8.6% vs 4.5%, p < 0.001). In particular, there was a higher frequency of E2F3 amplification in metastases (30% vs 7%, p = 0.046). Paired primary and metastatic tissue was available for 11 patients and 3 of these had amplifications of potential clinical relevance in metastases that were not in the primary tumor including ERBB2, CDK4, CCND1, E2F3, and AKT1. The transcriptional activity of these amplifications was supported by RNA expression data.The discordance in alterations between primary and metastatic tissue may be of clinical relevance in the era of genomically directed precision cancer medicine.

  View details for DOI 10.1186/s12885-015-1192-2

  View details for Web of Science ID 000352603600001

  View details for PubMedID 25886454

  View details for PubMedCentralID PMC4392457

• Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Perry, J. A., Kiezun, A., Tonzi, P., Van Allen, E. M., Carter, S. L., Baca, S. C., Cowley, G. S., Bhatt, A. S., Rheinbay, E., Pedamallu, C. S., Helman, E., Taylor-Weiner, A., McKenna, A., DeLuca, D. S., Lawrence, M. S., Ambrogio, L., Sougnez, C., Sivachenko, A., Walensky, L. D., Wagle, N., Mora, J., de Torres, C., Lavarino, C., Aguiar, S. d., Yunes, J. A., Brandalise, S. R., Mercado-Celis, G. E., Melendez-Zajgla, J., Cardenas-Cardos, R., Velasco-Hidalgo, L., Roberts, C. W., Garraway, L. A., Rodriguez-Galindo, C., Gabriel, S. B., Lander, E. S., Golub, T. R., Orkin, S. H., Getz, G., Janeway, K. A. 2014; 111 (51): E5564-E5573

  Abstract

  Osteosarcoma is the most common primary bone tumor, yet there have been no substantial advances in treatment or survival in three decades. We examined 59 tumor/normal pairs by whole-exome, whole-genome, and RNA-sequencing. Only the TP53 gene was mutated at significant frequency across all samples. The mean nonsilent somatic mutation rate was 1.2 mutations per megabase, and there was a median of 230 somatic rearrangements per tumor. Complex chains of rearrangements and localized hypermutation were detected in almost all cases. Given the intertumor heterogeneity, the extent of genomic instability, and the difficulty in acquiring a large sample size in a rare tumor, we used several methods to identify genomic events contributing to osteosarcoma survival. Pathway analysis, a heuristic analytic algorithm, a comparative oncology approach, and an shRNA screen converged on the phosphatidylinositol 3-kinase/mammalian target of rapamycin (PI3K/mTOR) pathway as a central vulnerability for therapeutic exploitation in osteosarcoma. Osteosarcoma cell lines are responsive to pharmacologic and genetic inhibition of the PI3K/mTOR pathway both in vitro and in vivo.

  View details for DOI 10.1073/pnas.1419260111

  View details for Web of Science ID 000346767200013

  View details for PubMedID 25512523

  View details for PubMedCentralID PMC4280630

• Bacillus Cereus: A Leukemia-Specific, Neuroinvasive Pathogen? Rhee, C., Manzo, V., Shea, T., Desjardins, C., van der Auwera, G., Young, S., Riley, A., DeAngelo, D. J., Baden, L. R., Gee, J., Meyerson, M., Klompas, M., Yokoe, D., Weiser, L., Pedamallu, C., Bhatt, A. S. AMER SOC HEMATOLOGY. 2014

  View details for Web of Science ID 000349242707200

• In Search of a Candidate Pathogen for Giant Cell Arteritis: Sequencing-Based Characterization of the Giant Cell Arteritis Microbiome ARTHRITIS & RHEUMATOLOGY Bhatt, A. S., Manzo, V. E., Pedamallu, C. S., Duke, F., Cai, D., Bienfang, D. C., Padera, R. F., Meyerson, M., Docken, W. P. 2014; 66 (7): 1939-1944

  Abstract

  To characterize the microbiome of the temporal artery in patients with giant cell arteritis (GCA), and to apply an unbiased and comprehensive shotgun sequencing-based approach to determine whether there is an enrichment of candidate pathogens in the affected tissue.Temporal artery biopsy specimens were collected from patients at a single institution over a period of 4 years, and unbiased DNA sequencing was performed on 17 formalin-fixed, paraffin-embedded specimens. Twelve of the 17 patients fulfilled the clinical and histopathologic criteria for GCA, and the other 5 patients served as controls. Using PathSeq software, human DNA sequences were computationally subtracted, and the remaining non-human DNA sequences were taxonomically classified using a comprehensive microbial sequence database. The relative abundance of microbes was inferred based on read counts assigned to each organism. Comparison of the microbial diversity between GCA cases and controls was carried out using hierarchical clustering and linear discriminant analysis of effect size.Propionibacterium acnes and Escherichia coli were the most abundant microorganisms in 16 of the 17 samples, and Moraxella catarrhalis was the most abundant organism in 1 control sample. Pathogens previously described to be correlated with GCA were not differentially abundant in cases compared to controls. There was not a significant burden of likely pathogenic viruses.DNA sequencing of temporal artery biopsy specimens from GCA cases, in comparison with non-GCA controls, showed no evidence of previously identified candidate GCA pathogens. A single pathogen was not clearly and consistently associated with GCA in this case series.

  View details for DOI 10.1002/art.38631

  View details for Web of Science ID 000339092800029

  View details for PubMedID 24644069

  View details for PubMedCentralID PMC4113339

• Comprehensive molecular characterization of urothelial bladder carcinoma NATURE Weinstein, J. N., Akbani, R., Broom, B. M., Wang, W., Verhaak, R. G., McConkey, D., Lerner, S., Morgan, M., Creighton, C. J., Smith, C., Kwiatkowski, D. J., Cherniack, A. D., Kim, J., Pedamallu, C. S., Noble, M. S., Al-Ahmadie, H. A., Reuter, V. E., Rosenberg, J. E., Bajorin, D. F., Bochner, B. H., Solit, D. B., Koppie, T., Robinson, B., Gordenin, D. A., Fargo, D., Klimczak, L. J., Roberts, S. A., Au, J., Laird, P. W., Hinoue, T., Schultz, N., Ramirez, R., Hansel, D., Hoadley, K. A., Kim, W. Y., Damrauer, J. S., Baylin, S. B., Mungall, A. J., Robertson, A. G., Chu, A., Kwiatkowski, D. J., Sougnez, C., Cibulskis, K., Lichtenstein, L., Sivachenko, A., Stewart, C., Lawrence, M. S., Getz, G., Lander, E., Gabriel, S. B., Creighton, C. J., Donehower, L., Cherniack, A. D., Kim, J., Carter, S. L., Saksena, G., Schumacher, S. E., Sougnez, C., Freeman, S. S., Jung, J., Pedamallu, C. S., Bhatt, A. S., Pugh, T., Getz, G., Beroukhim, R., Gabriel, S. B., Meyerson, M., Mungall, A. J., Robertson, A. G., Chu, A., Ally, A., Balasundaram, M., Butterfield, Y. S., Dhalla, N., Hirst, C., Holt, R. A., Jones, S. J., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Wong, T., Wye, N., Bowlby, R., Chuah, E., Guin, R., Jones, S. J., Marra, M. A., Hinoue, T., Shen, H., Bootwalla, M. S., Triche, T., Lai, P. H., Van den Berg, D. J., Weisenberger, D. J., Laird, P. W., Hansel, D., Hoadley, K. A., Balu, S., Bodenheimer, T., Damrauer, J. S., Hoyle, A. P., Jefferys, S. R., Meng, S., Mose, L. E., Simons, J. V., Soloway, M. G., Wu, J., Kim, W. Y., Parker, J. S., Hayes, D. N., Roach, J., Buda, E., Jones, C. D., Mieczkowski, P. A., Tan, D., Veluvolu, U., Waring, S., Auman, J. T., Perou, C. M., Wilkerson, M. D., Santoso, N., Parfenov, M., Ren, X., Pantazi, A., Hadjipanayis, A., Seidman, J., Kucherlapati, R., Lee, S., Yang, L., Park, P. J., Baylin, S. B., Xu, A. W., Protopopov, A., Zhang, J., Bristow, C., Mahadeshwar, H. S., Seth, S., Song, X., Tang, J., Zeng, D., Chin, L., Guo, C., Weinstein, J. N., Akbani, R., Broom, B. M., McConkey, D., Casasent, T. D., Liu, W., Ju, Z., Motter, T., Peng, B., Ryan, M., Wang, W., Verhaak, R. G., Su, X., Yang, J., Lorenzi, P. L., Yao, H., Zhang, N., Zhang, J., Mills, G. B., Kim, J., Noble, M. S., Cho, J., DiCara, D., Frazer, S., Gehlenborg, N., Heiman, D. I., Lin, P., Liu, Y., Stojanov, P., Voet, D., Zhang, H., Zou, L., Chin, L., Getz, G., Bernard, B., Kreisberg, D., Reynolds, S., Rovira, H., Shmulevich, I., Ramirez, R., Schultz, N., Gao, J., Jacobsen, A., Aksoy, B. A., Antipin, Y., Ciriello, G., Dresdner, G., Gross, B., Lee, W., Reva, B., Shen, R., Sinha, R., Sumer, S. O., Weinhold, N., Ladanyi, M., Sander, C., Benz, C., Carlin, D., Haussler, D., Ng, S., Paull, E. O., Stuart, J., Zhu, J., Liu, Y., Zhang, W., Taylor, B. S., Lichtenberg, T. M., Zmuda, E., Barr, T., Black, A. D., George, M., Hanf, B., Helsel, C., McAllister, C., Ramirez, N. C., Tabler, T. R., Weaver, S., Wise, L., Bowen, J., Gastier-Foster, J. M., Weinstein, J. N., Lerner, S., Jian, W., Tello, S., Ittman, M., Castro, P., McClenden, W. D., Morgan, M., Gibbs, R., Liu, Y., Saller, C., Tarvin, K., DiPiero, J. M., Owens, J., Bollag, R., Li, Q., Weinberger, P., Czerwinski, C., Huelsenbeck-Dill, L., Iacocca, M., Petrelli, N., Rabeno, B., Swanson, P., Shelton, T., Curley, E., Gardner, J., Mallery, D., Penny, R., Nguyen Van Bang, N. V., Phan Thi Hanh, P. T., Kohl, B., Xuan Van Le, X. V., Bui Duc Phu, B. D., Thorp, R., Nguyen Viet Tien, N. V., Le Quang Vinh, L. Q., Sandusky, G., Burks, E., Christ, K., Gee, J., Holway, A., Moinzadeh, A., Sorcini, A., Sullivan, T., Al-Ahmadie, H. A., Bajorin, D. F., Bochner, B. H., Garcia-Grossman, I. R., Regazzi, A. M., Solit, D. B., Rosenberg, J. E., Reuter, V. E., Koppie, T., Boice, L., Rathmell, W. K., Thorne, L., Bastacky, S., Davies, B., Dhir, R., Gingrich, J., Hrebinko, R., Maranchie, J., Nelson, J., Parwani, A., Bshara, W., Gaudioso, C., Morrison, C., Alexopoulou, V., Bartlett, J., Engel, J., Kodeeswaran, S., Antic, T., O'Donnell, P. H., Smith, N. D., Steinberg, G. D., Egea, S., Gomez-Fernandez, C., Herbert, L., Jorda, M., Soloway, M., Beaver, A., Carter, S., Kapur, P., Lewis, C., Lotan, Y., Robinson, B., Hansel, D., Guo, C., Bondaruk, J., Czerniak, B., Akbani, R., Broom, B. M., Liu, Y., Zhang, W., Weinstein, J. N., Lerner, S., Morgan, M., Kim, J., Cherniack, A. D., Freeman, S. S., Pedamallu, C. S., Noble, M. S., Kwiatkowski, D. J., Al-Ahmadie, H. A., Bajorin, D. F., Bochner, B. H., Solit, D. B., Rosenberg, J. E., Reuter, V. E., Koppie, T., Robinson, B., Skinner, E., Ramirez, R., Schultz, N., Hansel, D., Kim, W. Y., Guo, C., Bondaruk, J., Aldape, K., Czerniak, B., Jensen, M. A., Kahn, A. B., Pihl, T. D., Pot, D. A., Srinivasan, D., Wan, Y., Ferguson, M. L., Zenklusen, J. C., Davidsen, T., Demchok, J. A., Shaw, K. R., Sheth, M., Tarnuzzer, R., Wang, Z., Yang, L., Hutter, C., Ozenberger, B. A., Sofia, H. J., Eley, G. 2014; 507 (7492): 315-322

  View details for DOI 10.1038/nature12965

  View details for Web of Science ID 000333029000025

• Sequence-Based Discovery of Bradyrhizobium enterica in Cord Colitis Syndrome NEW ENGLAND JOURNAL OF MEDICINE Bhatt, A. S., Freeman, S. S., Herrera, A. F., Pedamallu, C. S., Gevers, D., Duke, F., Jung, J., Michaud, M., Walker, B. J., Young, S., Earl, A. M., Kostic, A. D., Ojesina, A. I., Hasserjian, R., Ballen, K. K., Chen, Y., Hobbs, G., Antin, J. H., Soiffer, R. J., Baden, L. R., Garrett, W. S., Hornick, J. L., Marty, F. M., Meyerson, M. 2013; 369 (6): 517-528

  Abstract

  Immunosuppression is associated with a variety of idiopathic clinical syndromes that may have infectious causes. It has been hypothesized that the cord colitis syndrome, a complication of umbilical-cord hematopoietic stem-cell transplantation, is infectious in origin.We performed shotgun DNA sequencing on four archived, paraffin-embedded endoscopic colon-biopsy specimens obtained from two patients with cord colitis. Computational subtraction of human and known microbial sequences and assembly of residual sequences into a bacterial draft genome were performed. We used polymerase-chain-reaction (PCR) assays and fluorescence in situ hybridization to determine whether the corresponding bacterium was present in additional patients and controls.DNA sequencing of the biopsy specimens revealed more than 2.5 million sequencing reads that did not match known organisms. These sequences were computationally assembled into a 7.65-Mb draft genome showing a high degree of homology with genomes of bacteria in the bradyrhizobium genus. The corresponding newly discovered bacterium was provisionally named Bradyrhizobium enterica. PCR identified B. enterica nucleotide sequences in biopsy specimens from all three additional patients with cord colitis whose samples were tested, whereas B. enterica sequences were absent in samples obtained from healthy controls and patients with colon cancer or graft-versus-host disease.We assembled a novel bacterial draft genome from the direct sequencing of tissue specimens from patients with cord colitis. Association of these sequences with cord colitis suggests that B. enterica may be an opportunistic human pathogen. (Funded by the National Cancer Institute and others.)

  View details for DOI 10.1056/NEJMoa1211115

  View details for Web of Science ID 000322842000008

  View details for PubMedID 23924002

  View details for PubMedCentralID PMC3889161

• NK-Cell and B-Cell Deficiency with a Thymic Mass NEW ENGLAND JOURNAL OF MEDICINE Ng, S., Fanta, C., Okam, M., Bhatt, A. S. 2011; 364 (6): 586-588

  View details for Web of Science ID 000287139900041

  View details for PubMedID 21306273

• MT-SP1 proteolysis and regulation of cell-microenvironment interactions FRONTIERS IN BIOSCIENCE-LANDMARK Darragh, M. R., Bhatt, A. S., Craik, C. S. 2008; 13: 528-539

  Abstract

  MT-SP1 is a type II transmembrane serine protease implicated in a range of human cancers including those of the breast, cervix, ovaries, prostate, colon and gastrointestinal tract. Mouse models have shown it to be critical for proper epidermal development and postnatal survival. However, the role of this enzyme in normal and malignant biology has not yet been fully elucidated. Several groups have identified putative substrates of MT-SP1 in an effort to understand the possible biological processes in which this protease may be involved. Methods for substrate identification include comparing known protein cleavage sequences with MT-SP1 specificity data, in vitro cleavage assays, examining genetic microarrays for enzyme/substrate coexpression, immunohistochemistry for colocalization, and a variety of phenotypic observations using cell culture and mouse models. Given the inherent limitations of each individual method, substrate plausibility is best substantiated using a combination of experimental approaches. Here we review MT-SP1 substrates identified to date and the possible physiological implications of substrate cleavage in cell-microenvironment interactions. This data indicates that MT-SP1 is capable of playing roles in growth factor activation, receptor activation and inactivation, protease activation, and ectodomain shedding. We also present for the first time vascular endothelial growth factor receptor 2 (VEGFR-2) as a putative substrate for MT-SP1.

  View details for DOI 10.2741/2698

  View details for Web of Science ID 000255775700042

  View details for PubMedID 17981566

• Coordinate expression and functional profiling identify an extracellular proteolytic signaling pathway PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Bhatt, A. S., Welm, A., Farady, C. J., Vasquez, M., Wilson, K., Craik, C. S. 2007; 104 (14): 5771-5776

  Abstract

  A multidisciplinary method combining transcriptional data, specificity profiling, and biological characterization of an enzyme may be used to predict novel substrates. By integrating protease substrate profiling with microarray gene coexpression data from nearly 2,000 human normal and cancerous tissue samples, three fundamental components of a protease-activated signaling pathway were identified. We find that MT-SP1 mediates extracellular signaling by regulating the local activation of the prometastatic growth factor MSP-1. We demonstrate MT-SP1 expression in peritoneal macrophages, and biochemical methods confirm the ability of MT-SP1 to cleave and activate pro-MSP-1 in vitro and in a cellular context. MT-SP1 induced the ability of MSP-1 to inhibit nitric oxide production in bone marrow macrophages. Addition of HAI-1 or an MT-SP1-specific antibody inhibitor blocked the proteolytic activation of MSP-1 at the cell surface of peritoneal macrophages. Taken together, our work indicates that MT-SP1 is sufficient for MSP-1 activation and that MT-SP1, MSP-1, and the previously shown MSP-1 tyrosine kinase receptor RON are required for peritoneal macrophage activation. This work shows that this triad of growth factor, growth factor activator protease, and growth factor receptor is a protease-activated signaling pathway. Individually, MT-SP1 and RON overexpression have been implicated in cancer progression and metastasis. Transcriptional coexpression of these genes suggests that this signaling pathway may be involved in several human cancers.

  View details for DOI 10.1073/pnas.0606514104

  View details for Web of Science ID 000245657600015

  View details for PubMedID 17389401

  View details for PubMedCentralID PMC1838401

• Hepatocyte growth factor is a preferred in vitro substrate for human hepsin, a membrane-anchored serine protease implicated in prostate and ovarian cancers BIOCHEMICAL JOURNAL Herter, S., Piper, D. E., Aaron, W., Gabriele, T., Cutler, G., Cao, P., Bhattt, A. S., Choe, Y., CRAIK, C. S., Walker, N., Meininger, D., Hoey, T., Austin, R. J. 2005; 390: 125-136

  Abstract

  Hepsin is a membrane-anchored, trypsin-like serine protease with prominent expression in the human liver and tumours of the prostate and ovaries. To better understand the biological functions of hepsin, we identified macromolecular substrates employing a tetrapeptide PS-SCL (positional scanning-synthetic combinatorial library) screen that rapidly determines the P1-P4 substrate specificity. Hepsin exhibited strong preference at the P1 position for arginine over lysine, and favoured threonine, leucine or asparagine at the P2, glutamine or lysine at the P3, and proline or lysine at the P4 position. The relative activity of hepsin toward individual AMC (7-amino-4-methylcoumarin)-tetrapeptides was generally consistent with the overall peptide profiling results derived from the PC-SCL screen. The most active tetrapeptide substrate Ac (acetyl)-KQLR-AMC matched with the activation cleavage site of the hepatocyte growth factor precursor sc-HGF (single-chain HGF), KQLR downward arrowVVNG (where downward arrow denotes the cleavage site), as identified by a database analysis of trypsin-like precursors. X-ray crystallographic studies with KQLR chloromethylketone showed that the KQLR peptide fits well into the substrate-binding cleft of hepsin. This hepsin-processed HGF induced c-Met receptor tyrosine phosphorylation in SKOV-3 ovarian cancer cells, indicating that the hepsin-cleaved HGF is biologically active. Activation cleavage site mutants of sc-HGF with predicted non-preferred sequences, DPGR downward arrowVVNG or KQLQ downward arrowVVNG, were not processed, illustrating that the P4-P1 residues can be important determinants for substrate specificity. In addition to finding macromolecular hepsin substrates, the extracellular inhibitors of the HGF activator, HAI-1 and HAI-2, were potent inhibitors of hepsin activity (IC50 4+/-0.2 nM and 12+/-0.5 nM respectively). Together, our findings suggest that the HGF precursor is a potential in vivo substrate for hepsin in tumours, where hepsin expression is dysregulated and may influence tumorigenesis through inappropriate activation and/or regulation of HGF receptor (c-Met) functions.

  View details for DOI 10.1042/BJ20041955

  View details for Web of Science ID 000231492800014

  View details for PubMedID 15839837

  View details for PubMedCentralID PMC1184568

• Adhesion signaling by a novel mitotic substrate of src kinases ONCOGENE Bhatt, A. S., Erdjument-Bromage, H., Tempst, P., CRAIK, C. S., Moasser, M. M. 2005; 24 (34): 5333-5343

  Abstract

  Src kinases are activated and relocalize to the cytoplasm during mitosis, but their mitotic function has remained elusive. We describe here a novel mitotic substrate of src kinases. Trask (transmembrane and associated with src kinases) is a 140 kDa type I transmembrane glycoprotein unrelated to currently known protein families. Src kinases phosphorylate Trask in vitro and mediate its mitotic hyperphosphorylation in vivo. Trask associates with both yes and src, is localized to the cell membrane during interphase, and undergoes cytoplasmic relocalization during mitosis. Overexpression of Trask leads to cell rounding and a loss of adhesion phenotype. Consistent with a function in cell adhesion, Trask interacts with a number of adhesion and matrix proteins including cadherins, syndecans, and the membrane-type serine protease 1 (MT-SP1), and is proteolytically cleaved by MT-SP1. Trask is unique among cell adhesion molecules in that it is under cell cycle regulation and thus links src kinases with the mitotic regulation of cell adhesion. This suggests a potential pathway by which hyperactive src kinases in tumors can deregulate adhesion signaling and mediate the metastatic phenotype.

  View details for DOI 10.1038/sj.onc.1208582

  View details for Web of Science ID 000231158500007

  View details for PubMedID 16007225

  View details for PubMedCentralID PMC3023961

• Substrates of the prostate-specific serine protease prostase/KLK4 defined by positional-scanning peptide libraries PROSTATE Matsumura, M., Bhatt, A. S., Andress, D., Clegg, N., Takayama, T. K., CRAIK, C. S., Nelson, P. S. 2005; 62 (1): 1-13

  Abstract

  Prostase/KLK4 is a member of the human kallikrein (KLK) gene family that is expressed in prostate epithelial cells under the regulation of androgenic hormones. In this study, we sought to characterize the substrate specificity of KLK4 in order to gain insight into potential physiological roles of the enzyme.A chimeric form of KLK4 was constructed in which the pro-region of KLK4 was replaced with the signal and propeptide sequence of trypsinogen (proT-KLK4) to create an activation site susceptible to enterokinase cleavage. proT-KLK4 was expressed in Drosophila S2 cells, purified, and activated with enterokinase to generate mature KLK4. The extended substrate specificity of KLK4 was defined by screening tetrapeptide positional scanning synthetic combinatorial libraries (PS-SCL).The preferred P1-P4 positions as determined by PS-SCL were: P1-Arg; P2-Gln/Leu/Val; P3-Gln/Ser/Val; P4-Ile/Val. The trypsin-like specificity of KLK4 was further confirmed using synthetic chromogenic peptides. Based upon the optimal cleavage site residues, a database search for potential KLK4 substrates identified several proteins with potential roles mediating normal prostate physiology or neoplastic growth including KLK3/PSA, parathyroid hormone-related peptide (PTHrP), and members of the bone morphogenetic protein (BMP) family. Recombinant KLK4 was able to activate pro-PSA/KLK3 and degrade members of the insulin-like growth factor (IGF) binding protein (IGFBP) family.These results identify potential KLK4 substrates that may serve to define the role of this protease in normal prostate physiology, and facilitate studies of the consequences of KLK4 expression in pathological conditions.

  View details for DOI 10.1002/pros.20101

  View details for Web of Science ID 000225704700001

  View details for PubMedID 15389820

• Quantitation of membrane type serine protease 1 (MT-SP1) in transformed and normal cells BIOLOGICAL CHEMISTRY Bhatt, A. S., Takeuchi, T., Ylstra, B., Ginzinger, D., Albertson, D., Shuman, M. A., CRAIK, C. S. 2003; 384 (2): 257-266

  Abstract

  Membrane type serine protease 1 (MT-SP1) is a representative member of a large family of related enzymes known as type II transmembrane serine proteases or membrane type serine proteases. MT-SP1 has been implicated in the selective proteolysis of key extracellular substrates but its physiological role is still not fully understood. MT-SP1 expression at the protein and RNA level has been previously examined by nonquantitative methods such as in situ hybridization, Northern blotting and immunohistochemistry. To establish an introductory understanding of the quantitative mRNA expression of MT-SP1 and to correlate these levels with urokinase-type plasminogen activator receptor (uPAR), a key component of extracellular proteolysis, quantitative RT-PCR was carried out. RNA expression was analyzed in 34 human cancer cell lines, 26 human tissues and 18 primary human breast cancer tissue samples. MT-SP1 mRNA is highly expressed in many breast, ovarian, prostate and colon cancer cell lines and normal human tissues of endodermal origin. At the transcript level, MT-SP1 shows a highly statistically significant correlation (Pearson's product moment correlation r = 0.784, p < 0.001) with uPAR in human breast cancer tissue. The exact role of MT-SP1 in concert with proteins such as uPAR and other members of the plasminogen activator cascade has yet to be ascertained. However, the significant correlation between MT-SP1 and uPAR transcript levels in this initial study suggests further work to establish the role of MT-SP1 as a possible prognostic, diagnostic or therapeutic target for breast cancer.

  View details for Web of Science ID 000181175000010

  View details for PubMedID 12675519