Rachael Chanin
Postdoctoral Scholar, Hematology
Contact
https://orcid.org/0000-0002-4625-356XAll Publications
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Long-read metagenomics reveals phage dynamics in the human gut microbiome.
Nature
2025
Abstract
Gut bacteriophages profoundly impact microbial ecology and health1-3; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations4. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain5. Finally, we describe a new class of 'IScream phages', which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.
View details for DOI 10.1038/s41586-025-09786-2
View details for PubMedID 41299176
View details for PubMedCentralID 5520141
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Clostridium cuniculi is associated with chronic high-morbidity low-mortality diarrhea in NSG and NSG-related mouse strains.
Veterinary pathology
2025: 3009858251372565
Abstract
In October 2020, adult male and female NSG (NOD. Cg-Prkdcscid Il2rgtm1Wjl/Sz) mice were reported for diarrhea within a mouse barrier facility. Other immunodeficient strains harboring the SCID (Prkdcscid) or Rag (Ragnull) mutations together with the IL2rg (Il2rgnull) mutation were affected. At its peak, over 20 laboratories in 10/16 (62.5%) barrier rooms were affected. Mortality was rare except in lactating females (≥ P11). Grossly, nonlactating adult female and male mice (n = 16) had mild to moderate, small and large intestinal distension with corresponding individual cell death and sloughing of superficial enterocytes in the cecocolonic mucosa. Lactating NSG dams (n=6) had moderate to severe gastrointestinal distension and/or segmental, dark red to gray, small intestinal discoloration. In addition to the same histologic lesions seen in nonlactating female NSG mice, lactating NSG dams often had severe ulcerative inflammation affecting the jejunum, ileum, cecum, and colon. Traditional ancillary diagnostic tests including aerobic and anaerobic cultures (blood, liver, spleen, and intestines), fecal PCR, and fecal floatation failed to yield a causative organism. Further cohousing and oral gavage studies determined neither immunocompetent CD1 (Crl:CD1 [ICR]) mice nor immunodeficient NOD scid (NOD.Cg-Prkdcscid/J) and Rag2 KO (C57BL/6. Cg-Rag2tm1.1Cgn/J) mice were susceptible to clinical disease. Extensive control barriers were implemented including a veterinary-managed NSG breeding barrier, alterations in husbandry practices, and strategic environmental disinfection, allowing for continuity of experimental studies while avoiding widespread depopulation of the barrier. Subsequent strain-resolved metagenomics and qPCR assay development identified Clostridium cuniculi and its enterotoxin exclusively within diarrheic mice.
View details for DOI 10.1177/03009858251372565
View details for PubMedID 40974275
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Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics.
bioRxiv : the preprint server for biology
2025
Abstract
Gut bacteriophages profoundly impact microbial ecology and human health, yet they are greatly understudied. Using deep, long-read bulk metagenomic sequencing, a technique that overcomes fundamental limitations of short-read approaches, we tracked prophage integration dynamics in 12 longitudinal stool samples from six healthy individuals, spanning a two-year timescale. While most prophages remain stably integrated into their host over two years, we discover that ~5% of phages are dynamically gained or lost from persistent bacterial hosts. Within the same sample, we find evidence of population heterogeneity in which identical bacterial hosts with and without a given integrated prophage coexist simultaneously. Furthermore, we demonstrate that phage induction, when detected, occurs predominantly at low levels (1-3x coverage compared to the host region). Interestingly, we identify multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phage are specific to a host of a given species or strain. Lastly, we describe a new class of phages, which we name "IScream phages". These phages co-opt bacterial IS30 transposases to mediate their integration, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity in this ecosystem.
View details for DOI 10.1101/2025.05.09.652943
View details for PubMedID 40654884
View details for PubMedCentralID PMC12247996
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Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.
Microbiome
2025; 13 (1): 71
Abstract
Bacteria use invertible genetic elements known as invertons to generate heterogeneity among a population and adapt to new and changing environments. In human gut bacteria, invertons are often found near genes associated with cell surface modifications, suggesting key roles in modulating dynamic processes such as surface adhesion and intestinal colonization. However, comprehensive testing of this hypothesis across complex bacterial communities like the human gut microbiome remains challenging. Metagenomic sequencing holds promise for detecting inversions without isolation and culturing, but ambiguity in read alignment limits the accuracy of the resulting inverton predictions.Here, we developed a customized bioinformatic workflow-PhaseFinderDC-to identify and track invertons in metagenomic data. Applying this method to a defined yet complex gut community (hCom2) across different growth environments over time using both in vitro and in vivo metagenomic samples, we detected invertons in most hCom2 strains. These include invertons whose orientation probabilities change over time and are statistically associated with environmental conditions. We used motif enrichment to identify putative inverton promoters and predict genes regulated by inverton flipping during intestinal colonization and surface adhesion. Analysis of inverton-proximal genes also revealed candidate invertases that may regulate flipping of specific invertons.Collectively, these findings suggest that surface adhesion and intestinal colonization in complex gut communities directly modulate inverton dynamics, offering new insights into the genetic mechanisms underlying these processes. Video Abstract.
View details for DOI 10.1186/s40168-025-02052-7
View details for PubMedID 40059174
View details for PubMedCentralID PMC11892184
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Intragenic DNA inversions expand bacterial coding capacity.
Nature
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
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Formate oxidation in the intestinal mucus layer enhances fitness of Salmonella enterica serovar Typhimurium
MBIO
2023: e0092123
Abstract
Salmonella enterica serovar Typhimurium induces intestinal inflammation to create a niche that fosters the outgrowth of the pathogen over the gut microbiota. Under inflammatory conditions, Salmonella utilizes terminal electron acceptors generated as byproducts of intestinal inflammation to generate cellular energy through respiration. However, the electron donating reactions in these electron transport chains are poorly understood. Here, we investigated how formate utilization through the respiratory formate dehydrogenase-N (FdnGHI) and formate dehydrogenase-O (FdoGHI) contribute to gut colonization of Salmonella. Both enzymes fulfilled redundant roles in enhancing fitness in a mouse model of Salmonella-induced colitis, and coupled to tetrathionate, nitrate, and oxygen respiration. The formic acid utilized by Salmonella during infection was generated by its own pyruvate-formate lyase as well as the gut microbiota. Transcription of formate dehydrogenases and pyruvate-formate lyase was significantly higher in bacteria residing in the mucus layer compared to the lumen. Furthermore, formate utilization conferred a more pronounced fitness advantage in the mucus, indicating that formate production and degradation occurred predominantly in the mucus layer. Our results provide new insights into how Salmonella adapts its energy metabolism to the local microenvironment in the gut. IMPORTANCE Bacterial pathogens must not only evade immune responses but also adapt their metabolism to successfully colonize their host. The microenvironments encountered by enteric pathogens differ based on anatomical location, such as small versus large intestine, spatial stratification by host factors, such as mucus layer and antimicrobial peptides, and distinct commensal microbial communities that inhabit these microenvironments. Our understanding of how Salmonella populations adapt its metabolism to different environments in the gut is incomplete. In the current study, we discovered that Salmonella utilizes formate as an electron donor to support respiration, and that formate oxidation predominantly occurs in the mucus layer. Our experiments suggest that spatially distinct Salmonella populations in the mucus layer and the lumen differ in their energy metabolism. Our findings enhance our understanding of the spatial nature of microbial metabolism and may have implications for other enteric pathogens as well as commensal host-associated microbial communities.
View details for DOI 10.1128/mbio.00921-23
View details for Web of Science ID 001037089500001
View details for PubMedID 37498116
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Chemoproteomic identification of a DPP4 homolog in Bacteroides thetaiotaomicron.
Nature chemical biology
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
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Intragenic DNA inversions expand bacterial coding capacity.
bioRxiv : the preprint server for biology
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
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Colonocyte-derived lactate promotes E. coli fitness in the context of inflammation-associated gut microbiota dysbiosis.
Microbiome
2022; 10 (1): 200
Abstract
BACKGROUND: Intestinal inflammation disrupts the microbiota composition leading to an expansion of Enterobacteriaceae family members (dysbiosis). Associated with this shift in microbiota composition is a profound change in the metabolic landscape of the intestine. It is unclear how changes in metabolite availability during gut inflammation impact microbial and host physiology.RESULTS: We investigated microbial and host lactate metabolism in murine models of infectious and non-infectious colitis. During inflammation-associated dysbiosis, lactate levels in the gut lumen increased. The disease-associated spike in lactate availability was significantly reduced in mice lacking the lactate dehydrogenase A subunit in intestinal epithelial cells. Commensal E. coli and pathogenic Salmonella, representative Enterobacteriaceae family members, utilized lactate via the respiratory L-lactate dehydrogenase LldD to increase fitness. Furthermore, mice lacking the lactate dehydrogenase A subunit in intestinal epithelial cells exhibited lower levels of inflammation in a model of non-infectious colitis.CONCLUSIONS: The release of lactate by intestinal epithelial cells during gut inflammation impacts the metabolism of gut-associated microbial communities. These findings suggest that during intestinal inflammation and dysbiosis, changes in metabolite availability can perpetuate colitis-associated disturbances of microbiota composition. Video Abstract.
View details for DOI 10.1186/s40168-022-01389-7
View details for PubMedID 36434690
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From genome structure to function: insights into structural variation in microbiology.
Current opinion in microbiology
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