Stanford Advisors

All Publications

  • Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities. bioRxiv : the preprint server for biology Goldman, D. A., Xue, K. S., Parrott, A. B., Jeeda, R. R., Franzese, L. R., Lopez, J. G., Vila, J. C., Petrov, D. A., Good, B. H., Relman, D. A., Huang, K. C. 2023


    The long-term success of introduced populations depends on their initial size and ability to compete against existing residents, but it remains unclear how these factors collectively shape colonization. Here, we investigate how initial population (propagule) size and resource competition interact during community coalescence by systematically mixing eight pairs of in vitro microbial communities at ratios that vary over six orders of magnitude, and we compare our results to a neutral ecological model. Although the composition of the resulting co-cultures deviated substantially from neutral expectations, each co-culture contained species whose relative abundance depended on propagule size even after ~40 generations of growth. Using a consumer-resource model, we show that this dose-dependent colonization can arise when resident and introduced species have high niche overlap and consume shared resources at similar rates. This model predicts that propagule size will have larger, longer-lasting effects in diverse communities in which niche overlap is higher, and we experimentally confirm that strain isolates show stronger dose dependence when introduced into diverse communities than in pairwise co-culture. This work shows how neutral-like colonization dynamics can emerge from non-neutral resource competition and have lasting effects on the outcomes of community coalescence.

    View details for DOI 10.1101/2023.11.29.569120

    View details for PubMedID 38076867

    View details for PubMedCentralID PMC10705444

  • Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation. bioRxiv : the preprint server for biology Xue, K. S., Walton, S. J., Goldman, D. A., Morrison, M. L., Verster, A. J., Parrott, A. B., Yu, F. B., Neff, N. F., Rosenberg, N. A., Ross, B. D., Petrov, D. A., Huang, K. C., Good, B. H., Relman, D. A. 2023


    Humans constantly encounter new microbes, but few become long-term residents of the adult gut microbiome. Classical theories predict that colonization is determined by the availability of open niches, but it remains unclear whether other ecological barriers limit commensal colonization in natural settings. To disentangle these effects, we used a controlled perturbation with the antibiotic ciprofloxacin to investigate the dynamics of gut microbiome transmission in 22 households of healthy, cohabiting adults. Colonization was rare in three-quarters of antibiotic-taking subjects, whose resident strains rapidly recovered in the week after antibiotics ended. In contrast, the remaining subjects exhibited lasting responses to antibiotics, with extensive species losses and transient expansions of potential opportunistic pathogens. These subjects experienced elevated rates of commensal colonization, but only after long delays: many new colonizers underwent sudden, correlated expansions months after the antibiotic perturbation. Furthermore, strains that had previously transmitted between cohabiting partners rarely recolonized after antibiotic disruptions, showing that colonization displays substantial historical contingency. This work demonstrates that there remain substantial ecological barriers to colonization even after major microbiome disruptions, suggesting that dispersal interactions and priority effects limit the pace of community change.

    View details for DOI 10.1101/2023.09.26.559480

    View details for PubMedID 37808827

    View details for PubMedCentralID PMC10557656

  • Linking influenza virus evolution within and between human hosts. Virus evolution Xue, K. S., Bloom, J. D. 2020; 6 (1): veaa010


    Influenza viruses rapidly diversify within individual human infections. Several recent studies have deep-sequenced clinical influenza infections to identify viral variation within hosts, but it remains unclear how within-host mutations fare at the between-host scale. Here, we compare the genetic variation of H3N2 influenza within and between hosts to link viral evolutionary dynamics across scales. Synonymous sites evolve at similar rates at both scales, indicating that global evolution at these putatively neutral sites results from the accumulation of within-host variation. However, nonsynonymous mutations are depleted between hosts compared to within hosts, suggesting that selection purges many of the protein-altering changes that arise within hosts. The exception is at antigenic sites, where selection detectably favors nonsynonymous mutations at the global scale, but not within hosts. These results suggest that selection against deleterious mutations and selection for antigenic change are the main forces that act on within-host variants of influenza virus as they transmit and circulate between hosts.

    View details for DOI 10.1093/ve/veaa010

    View details for PubMedID 32082616

  • Parallel evolution of influenza across multiple spatiotemporal scales ELIFE Xue, K. S., Stevens-Ayers, T., Campbell, A. P., Englund, J. A., Pergam, S. A., Boeckh, M., Bloom, J. D. 2017; 6


    Viral variants that arise in the global influenza population begin as de novo mutations in single infected hosts, but the evolutionary dynamics that transform within-host variation to global genetic diversity are poorly understood. Here, we demonstrate that influenza evolution within infected humans recapitulates many evolutionary dynamics observed at the global scale. We deep-sequence longitudinal samples from four immunocompromised patients with long-term H3N2 influenza infections. We find parallel evolution across three scales: within individual patients, in different patients in our study, and in the global influenza population. In hemagglutinin, a small set of mutations arises independently in multiple patients. These same mutations emerge repeatedly within single patients and compete with one another, providing a vivid clinical example of clonal interference. Many of these recurrent within-host mutations also reach a high global frequency in the decade following the patient infections. Our results demonstrate surprising concordance in evolutionary dynamics across multiple spatiotemporal scales.

    View details for DOI 10.7554/elife.26875

    View details for Web of Science ID 000404339400001

    View details for PubMedID 28653624

    View details for PubMedCentralID PMC5487208

  • Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture ELIFE Xue, K. S., Hooper, K. A., Odart, A. R., Dingens, A. S., Bloom, J. D. 2016; 5: e13974


    RNA viruses rapidly diversify into quasispecies of related genotypes. This genetic diversity has long been known to facilitate adaptation, but recent studies have suggested that cooperation between variants might also increase population fitness. Here, we demonstrate strong cooperation between two H3N2 influenza variants that differ by a single mutation at residue 151 in neuraminidase, which normally mediates viral exit from host cells. Residue 151 is often annotated as an ambiguous amino acid in sequenced isolates, indicating mixed viral populations. We show that mixed populations grow better than either variant alone in cell culture. Pure populations of either variant generate the other through mutation and then stably maintain a mix of the two genotypes. We suggest that cooperation arises because mixed populations combine one variant's proficiency at cell entry with the other's proficiency at cell exit. Our work demonstrates a specific cooperative interaction between defined variants in a viral quasispecies.

    View details for DOI 10.7554/eLife.13974

    View details for Web of Science ID 000371971800001

    View details for PubMedID 26978794

    View details for PubMedCentralID PMC4805539

  • Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron. BMC biology Arjes, H. A., Sun, J., Liu, H., Nguyen, T. H., Culver, R. N., Celis, A. I., Walton, S. J., Vasquez, K. S., Yu, F. B., Xue, K. S., Newton, D., Zermeno, R., Weglarz, M., Deutschbauer, A., Huang, K. C., Shiver, A. L. 2022; 20 (1): 285


    Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in early stages of development.Here, we describe the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community. We used flow cytometry to sort single cells from a pooled library, located mutants within this initial progenitor collection by applying a pooling strategy with barcode sequencing, and re-arrayed specific mutants to create a condensed collection with single-insertion strains covering >2500 genes. To demonstrate the potential of the condensed collection for phenotypic screening, we analyzed growth dynamics and cell morphology. We identified both growth defects and altered cell shape in mutants disrupting sphingolipid synthesis and thiamine scavenging. Finally, we analyzed the process of assembling the B. theta condensed collection to identify inefficiencies that limited coverage. We demonstrate as part of this analysis that the process of assembling an ordered collection can be accurately modeled using barcode sequencing data.We expect that utilization of this ordered collection will accelerate research into B. theta physiology and that lessons learned while assembling the collection will inform future efforts to assemble ordered mutant collections for an increasing number of gut microbiota members.

    View details for DOI 10.1186/s12915-022-01481-2

    View details for PubMedID 36527020

  • Optimization of the 16S rRNA sequencing analysis pipeline for studying invitro communities of gut commensals. iScience Celis, A. I., Aranda-Diaz, A., Culver, R., Xue, K., Relman, D., Shi, H., Huang, K. C. 2022; 25 (4): 103907


    While microbial communities inhabit a wide variety of complex natural environments, invitro culturing enables highly controlled conditions and high-throughput interrogation for generating mechanistic insights. Invitro assemblies of gut commensals have recently been introduced as models for the intestinal microbiota, which plays fundamental roles in host health. However, a protocol for 16S rRNA sequencing and analysis of invitro samples that optimizes financial cost, time/effort, and accuracy/reproducibility has yet to be established. Here, we systematically identify protocol elements that have significant impact, introduce bias, and/or can be simplified. Our results indicate that community diversity and composition are generally unaffected by substantial protocol streamlining. Additionally, we demonstrate that a strictly aerobic halophile is an effective spike-in for estimating absolute abundances in communities of anaerobic gut commensals. This time- and money-saving protocol should accelerate discovery by increasing 16S rRNA data reliability and comparability and through the incorporation of absolute abundance estimates.

    View details for DOI 10.1016/j.isci.2022.103907

    View details for PubMedID 35340431

  • REWRITING THE BIOLOGY OF DIFFERENCE How a Writing-Centered, Case-Based Curricular Approach Can Reform Undergraduate Science WRITING ACROSS DIFFERENCE Callow, M., Xue, K., Daniel, Malcolm, K., Rai, C. 2022: 116-135
  • Reconciling disparate estimates of viral genetic diversity during human influenza infections NATURE GENETICS Xue, K. S., Bloom, J. D. 2019; 51 (9): 1298–1301

    View details for DOI 10.1038/s41588-019-0349-3

    View details for Web of Science ID 000484010800002

    View details for PubMedID 30804564

    View details for PubMedCentralID PMC6708745

  • Sera from Individuals with Narrowly Focused Influenza Virus Antibodies Rapidly Select Viral Escape Mutations In Ovo JOURNAL OF VIROLOGY Davis, A. F., McCormick, K., Gumina, M. E., Petrie, J. G., Martin, E. T., Xue, K. S., Bloom, J. D., Monto, A. S., Bushman, F. D., Hensley, S. E. 2018; 92 (19)


    Influenza viruses use distinct antibody escape mechanisms depending on the overall complexity of the antibody response that is encountered. When grown in the presence of a hemagglutinin (HA) monoclonal antibody, influenza viruses typically acquire a single HA mutation that reduces the binding of that specific monoclonal antibody. In contrast, when confronted with mixtures of HA monoclonal antibodies or polyclonal sera that have antibodies that bind several HA epitopes, influenza viruses acquire mutations that increase HA binding to host cells. Recent data from our laboratory and others suggest that some humans possess antibodies that are narrowly focused on HA epitopes that were present in influenza virus strains that they were likely exposed to in childhood. Here, we completed a series of experiments to determine if humans with narrowly focused HA antibody responses are able to select for influenza virus antigenic escape variants in ovo We identified three human donors that possessed HA antibody responses that were heavily focused on a single HA antigenic site. Sera from all three of these donors selected single HA escape mutations during in ovo passage experiments, similar to what has been previously reported for single monoclonal antibodies. These single HA mutations directly reduced binding of serum antibodies used for selection. We propose that new antigenic variants of influenza viruses might originate in individuals who produce antibodies that are narrowly focused on HA epitopes that were present in viral strains that they encountered in childhood.IMPORTANCE Influenza vaccine strains must be updated frequently since circulating viral strains continuously change in antigenically important epitopes. Our previous studies have demonstrated that some individuals possess antibody responses that are narrowly focused on epitopes that were present in viral strains that they encountered during childhood. Here, we show that influenza viruses rapidly escape this type of polyclonal antibody response when grown in ovo by acquiring single mutations that directly prevent antibody binding. These studies improve our understanding of how influenza viruses evolve when confronted with narrowly focused polyclonal human antibodies.

    View details for DOI 10.1128/JVI.00859-18

    View details for Web of Science ID 000444430700014

    View details for PubMedID 30045982

    View details for PubMedCentralID PMC6146816

  • Within-Host Evolution of Human Influenza Virus TRENDS IN MICROBIOLOGY Xue, K. S., Moncla, L. H., Bedford, T., Bloom, J. D. 2018; 26 (9): 781–93


    The rapid global evolution of influenza virus begins with mutations that arise de novo in individual infections, but little is known about how evolution occurs within hosts. We review recent progress in understanding how and why influenza viruses evolve within human hosts. Advances in deep sequencing make it possible to measure within-host genetic diversity in both acute and chronic influenza infections. Factors like antigenic selection, antiviral treatment, tissue specificity, spatial structure, and multiplicity of infection may affect how influenza viruses evolve within human hosts. Studies of within-host evolution can contribute to our understanding of the evolutionary and epidemiological factors that shape influenza virus's global evolution.

    View details for DOI 10.1016/j.tim.2018.02.007

    View details for Web of Science ID 000441415900008

    View details for PubMedID 29534854

    View details for PubMedCentralID PMC6097882

  • Cooperating H3N2 Influenza Virus Variants A in Primary Clinical Samples MSPHERE Xue, K. S., Greninger, A. L., Perez-Osorio, A., Bloom, J. D. 2018; 3 (1)


    The high mutation rates of RNA viruses lead to rapid genetic diversification, which can enable cooperative interactions between variants in a viral population. We previously described two distinct variants of H3N2 influenza virus that cooperate in cell culture. These variants differ by a single mutation, D151G, in the neuraminidase protein. The D151G mutation reaches a stable frequency of about 50% when virus is passaged in cell culture. However, it is unclear whether selection for the cooperative benefits of D151G is a cell culture phenomenon or whether the mutation is also sometimes present at appreciable frequency in virus populations sampled directly from infected humans. Prior work has not detected D151G in unpassaged clinical samples, but those studies have used methods like Sanger sequencing and pyrosequencing, which are relatively insensitive to low-frequency variation. We identified nine samples of human H3N2 influenza virus collected between 2013 and 2015 in which Sanger sequencing had detected a high frequency of the D151G mutation following one to three passages in cell culture. We deep sequenced the unpassaged clinical samples to identify low-frequency viral variants. The frequency of D151G did not exceed the frequency of library preparation and sequencing errors in any of the sequenced samples. We conclude that passage in cell culture is primarily responsible for the frequent observations of D151G in recent H3N2 influenza virus strains. IMPORTANCE Viruses mutate rapidly, and recent studies of RNA viruses have shown that related viral variants can sometimes cooperate to improve each other's growth. We previously described two variants of H3N2 influenza virus that cooperate in cell culture. The mutation responsible for cooperation is often observed when human samples of influenza virus are grown in the lab before sequencing, but it is unclear whether the mutation also exists in human infections or is exclusively the result of lab passage. We identified nine human isolates of influenza virus that had developed the cooperating mutation after being grown in the lab and performed highly sensitive deep sequencing of the unpassaged clinical samples to determine whether the mutation existed in the original human infections. We found no evidence of the cooperating mutation in the unpassaged samples, suggesting that the cooperation arises primarily under laboratory conditions.

    View details for DOI 10.1128/mSphereDirect.00552-17

    View details for Web of Science ID 000425277500031

    View details for PubMedID 29299533

    View details for PubMedCentralID PMC5750391

  • Looking Deep inside Influenza Infections CELL SYSTEMS Xue, K. S., Bloom, J. D. 2017; 5 (1): 4
  • Selection on Meiosis Genes in Diploid and Tetraploid Arabidopsis arenosa MOLECULAR BIOLOGY AND EVOLUTION Wright, K. M., Arnold, B., Xue, K., Surinova, M., O'Connell, J., Bomblies, K. 2015; 32 (4): 944–55


    Meiotic chromosome segregation is critical for fertility across eukaryotes, and core meiotic processes are well conserved even between kingdoms. Nevertheless, recent work in animals has shown that at least some meiosis genes are highly diverse or strongly differentiated among populations. What drives this remains largely unknown. We previously showed that autotetraploid Arabidopsis arenosa evolved stable meiosis, likely through reduced crossover rates, and that associated with this there is strong evidence for selection in a subset of meiosis genes known to affect axis formation, synapsis, and crossover frequency. Here, we use genome-wide data to study the molecular evolution of 70 meiosis genes in a much wider sample of A. arenosa. We sample the polyploid lineage, a diploid lineage from the Carpathian Mountains, and a more distantly related diploid lineage from the adjacent, but biogeographically distinct Pannonian Basin. We find that not only did selection act on meiosis genes in the polyploid lineage but also independently on a smaller subset of meiosis genes in Pannonian diploids. Functionally related genes are targeted by selection in these distinct contexts, and in two cases, independent sweeps occurred in the same loci. The tetraploid lineage has sustained selection on more genes, has more amino acid changes in each, and these more often affect conserved or potentially functional sites. We hypothesize that Pannonian diploid and tetraploid A. arenosa experienced selection on structural proteins that mediate sister chromatid cohesion, the formation of meiotic chromosome axes, and synapsis, likely for different underlying reasons.

    View details for DOI 10.1093/molbev/msu398

    View details for Web of Science ID 000353560900009

    View details for PubMedID 25543117

    View details for PubMedCentralID PMC4379401

  • Laboratory divergence of Methylobacterium extorquens AM1 through unintended domestication and past selection for antibiotic resistance BMC MICROBIOLOGY Carroll, S., Xue, K. S., Marx, C. J. 2014; 14: 2


    A common assumption of microorganisms is that laboratory stocks will remain genetically and phenotypically constant over time, and across laboratories. It is becoming increasingly clear, however, that mutations can ruin strain integrity and drive the divergence or "domestication" of stocks. Since its discovery in 1960, a stock of Methylobacterium extorquens AM1 ("AM1") has remained in the lab, propagated across numerous growth and storage conditions, researchers, and facilities. To explore the extent to which this lineage has diverged, we compared our own "Modern" stock of AM1 to a sample archived at a culture stock center shortly after the strain's discovery. Stored as a lyophilized sample, we hypothesized that this Archival strain would better reflect the first-ever isolate of AM1 and reveal ways in which our Modern stock has changed through laboratory domestication or other means.Using whole-genome re-sequencing, we identified some 29 mutations - including single nucleotide polymorphisms, small indels, the insertion of mobile elements, and the loss of roughly 36 kb of DNA - that arose in the laboratory-maintained Modern lineage. Contrary to our expectations, Modern was both slower and less fit than Archival across a variety of growth substrates, and showed no improvement during long-term growth and storage. Modern did, however, outperform Archival during growth on nutrient broth, and in resistance to rifamycin, which was selected for by researchers in the 1980s. Recapitulating selection for rifamycin resistance in replicate Archival populations showed that mutations to RNA polymerase B (rpoB) substantially decrease growth in the absence of antibiotic, offering an explanation for slower growth in Modern stocks. Given the large number of genomic changes arising from domestication (28), it is somewhat surprising that the single other mutation attributed to purposeful laboratory selection accounts for much of the phenotypic divergence between strains.These results highlight the surprising degree to which AM1 has diverged through a combination of unintended laboratory domestication and purposeful selection for rifamycin resistance. Instances of strain divergence are important, not only to ensure consistency of experimental results, but also to explore how microbes in the lab diverge from one another and from their wild counterparts.

    View details for DOI 10.1186/1471-2180-14-2

    View details for Web of Science ID 000334718000001

    View details for PubMedID 24384040

    View details for PubMedCentralID PMC3926354

  • Genetic Adaptation Associated with Genome-Doubling in Autotetraploid Arabidopsis arenosa PLOS GENETICS Hollister, J. D., Arnold, B. J., Svedin, E., Xue, K. S., Dilkes, B. P., Bomblies, K. 2012; 8 (12): e1003093


    Genome duplication, which results in polyploidy, is disruptive to fundamental biological processes. Genome duplications occur spontaneously in a range of taxa and problems such as sterility, aneuploidy, and gene expression aberrations are common in newly formed polyploids. In mammals, genome duplication is associated with cancer and spontaneous abortion of embryos. Nevertheless, stable polyploid species occur in both plants and animals. Understanding how natural selection enabled these species to overcome early challenges can provide important insights into the mechanisms by which core cellular functions can adapt to perturbations of the genomic environment. Arabidopsis arenosa includes stable tetraploid populations and is related to well-characterized diploids A. lyrata and A. thaliana. It thus provides a rare opportunity to leverage genomic tools to investigate the genetic basis of polyploid stabilization. We sequenced the genomes of twelve A. arenosa individuals and found signatures suggestive of recent and ongoing selective sweeps throughout the genome. Many of these are at genes implicated in genome maintenance functions, including chromosome cohesion and segregation, DNA repair, homologous recombination, transcriptional regulation, and chromatin structure. Numerous encoded proteins are predicted to interact with one another. For a critical meiosis gene, ASYNAPSIS1, we identified a non-synonymous mutation that is highly differentiated by cytotype, but present as a rare variant in diploid A. arenosa, indicating selection may have acted on standing variation already present in the diploid. Several genes we identified that are implicated in sister chromatid cohesion and segregation are homologous to genes identified in a yeast mutant screen as necessary for survival of polyploid cells, and also implicated in genome instability in human diseases including cancer. This points to commonalities across kingdoms and supports the hypothesis that selection has acted on genes controlling genome integrity in A. arenosa as an adaptive response to genome doubling.

    View details for DOI 10.1371/journal.pgen.1003093

    View details for Web of Science ID 000312905600010

    View details for PubMedID 23284289

    View details for PubMedCentralID PMC3527224