Evolutionary dynamics of bacteria in the gut microbiome within and across hosts
[['The gut microbiome is a complex ecosystem comprised of a diverse array of microbial organisms .', 'The abundances of different species and strains can vary dramatically based on diet [1] , host species [2] , and the identities of other co-colonizing taxa [3] .', 'These rapid shifts in community composition suggest that individual gut microbes may be adapted to specific environmental conditions , with strong selection pressures between competing species or strains .', 'Yet , while these ecological responses have been extensively studied , much less is known about the evolutionary forces that operate within populations of gut bacteria , both within individual hosts and across the larger host-associated population .', 'This makes it difficult to predict how rapidly strains of gut microbes will evolve new ecological preferences when faced with environmental challenges , such as drugs or diet , and how the genetic composition of the community will change as a result .', 'The answers to these questions depend on two different types of information .', 'At a mechanistic level , one must understand the functional traits that are under selection in the gut and how they may be modified genetically .', 'Recent work has started to address this question , leveraging techniques from comparative genomics [4–6] , evolution in model organisms [7–9] , and high-throughput genetic screens [10 , 11] .', 'Yet , in addition to the targets of selection , evolution also depends on population genetic processes that describe how mutations spread through a population of gut bacteria , both within individual hosts and across the larger population .', 'These dynamical processes can strongly influence which mutations are likely to fix within a population , and the levels of genetic diversity that such populations can maintain .', 'Understanding these processes is the goal of our present work .', 'Previous studies of pathogens [12] , laboratory evolution experiments [13] , and some environmental communities [14–17] have shown that microbial evolutionary dynamics are often dominated by rapid adaptation , with new variants accumulating within months or years [7 , 14 , 18–25] .', 'However , it is not clear how this existing picture of microbial evolution extends to a more complex and established ecosystem like the healthy gut microbiome .', 'On the one hand , hominid gut bacteria have had many generations to adapt to their host environment [26] , and they may not be subjected to the same immune pressures as pathogens .', 'The large number of potential competitors in the gut ecosystem may also provide fewer opportunities for a strain to adapt to new conditions before an existing strain expands to fill the niche [27 , 28] or a new strain invades from outside the host .', 'On the other hand , it is also possible that small-scale environmental fluctuations , either driven directly by the host or through interactions with other resident strains , might increase the opportunities for local adaptation [29] .', 'If immigration is restricted , the large census population size of gut bacteria could allow residents to produce and fix adaptive variants rapidly before a new strain is able to invade .', 'In this case , one could observe rapid adaptation on short timescales , which is eventually arrested on longer timescales as strains are exposed to the full range of host environments .', 'Additional opportunities for adaptation can occur if the range of host environments also shifts over time ( e . g . , due to urbanization , antibiotic usage , etc . ) .', 'Determining which of these scenarios apply to gut communities is critical for efforts to study and manipulate the microbiome .', 'While traditional amplicon sequencing provides limited resolution to detect within-species evolution [30] , whole-genome shotgun metagenomic sequencing is starting to provide the raw polymorphism data necessary to address these questions [31] .', 'In particular , several reference-based approaches have been developed to detect genetic variants within individual species in larger metagenomic samples [31–36] .', 'While these approaches enable strain-level comparisons between samples , they have also documented substantial within-species variation in individual metagenomes [31 , 35 , 37] .', 'This makes it difficult to assign an evolutionary interpretation to the genetic differences between samples , because they arise from unobserved mixtures of different bacterial lineages .', 'Several approaches have been developed to further resolve these mixed populations into individual haplotypes or "strains . "', 'These range from simple consensus approximations [35 , 37 , 38] , to sophisticated clustering algorithms [39 , 40] and the incorporation of physical linkage information [41] .', 'However , while these methods are useful for tracking well-defined strains across samples , it is not known how their assumptions and failure modes might bias inferences of evolutionary dynamics , particularly among closely related strains .', 'As a result , the evolutionary processes that operate within species of gut bacteria remain poorly characterized .', 'In this study , we take a different approach to the strain detection problem that is specifically designed for inferring evolutionary dynamics in a large panel of metagenomes .', 'Building on earlier work by [4 , 35] , we show that many prevalent species have a subset of hosts for which a portion of the dominant lineage is much easier to identify .', 'By focusing only on this subset of samples , we develop methods for resolving small differences between the dominant lineages with a high degree of confidence .', 'We use this approach to analyze a large panel of publicly available human stool samples [42–46] , which allows us to quantify evolutionary dynamics within and across hosts in approximately 40 prevalent bacterial species .', 'We find that the long-term evolutionary dynamics across hosts are broadly consistent with models of quasi-sexual evolution and purifying selection , with relatively weak geographic structure in many prevalent species .', 'However , our quantitative approach also reveals interesting departures from standard population genetic models of these processes , suggesting that new models are required to fully understand the evolutionary dynamics that take place across the larger population .', 'We also use our approach to detect examples of within-host adaptation , in which nucleotide variants or gene gains or losses rapidly sweep to high frequency on 6-month timescales .', 'We find evidence that some within-host sweeps may be seeded by recombination , in addition to de novo mutations , as might be expected for a complex ecosystem with frequent horizontal exchange .', 'However , by analyzing differences between adult twins , we find that short-term evolution can eventually be overwhelmed by the invasion of distantly related strains on multi-decade timescales .', 'This suggests that resident strains are rarely able to become so well adapted to a particular host that they prevent future replacements .', 'Together , these results show that the gut microbiome is a promising system for studying the dynamics of microbial evolution in a complex community setting .', 'The framework we introduce may also be useful for characterizing evolution of microbial communities in other environments .'], ['To investigate evolutionary dynamics within species in the gut microbiome , we analyzed shotgun metagenomic data from a panel of stool samples from 693 healthy individuals sequenced in previous work ( S1 Table ) .', 'This panel includes 250 North American subjects sequenced by the Human Microbiome Project ( HMP ) [42 , 44] , a subset of which were sampled at 2 or 3 time points roughly 6–12 months apart .', 'To probe within-host dynamics on longer timescales , we also included data from a cohort of 125 pairs of adult twins from the TwinsUK registry [45] , and 4 pairs of younger twins from [46] .', 'As we describe below , the differences between these cohorts provide a proxy for the temporal changes that accumulate in adult twins over longer timescales .', 'Finally , to further control for geographic structure , we also included samples from 185 Chinese subjects sequenced at a single time point [43] .', 'We used a standard reference-based approach to measure single nucleotide variant ( SNV ) frequencies and gene copy number across a panel of prevalent species for each metagenomic sample ( see S1A Text for details on the bioinformatic pipeline , including mapping parameters and other filters ) .', 'Descriptive summaries of this genetic variation have been reported elsewhere [31 , 33–35 , 37 , 44] .', 'Here , we revisit these patterns to investigate how they emerge from the lineage structure set by the host colonization process .', 'Using these results , we then show how certain aspects of this lineage structure can be inferred from the statistics of within-host polymorphism , which enable measurements of evolutionary dynamics across samples .', 'As an illustrative example , we first focus on the patterns of polymorphism in Bacteroides vulgatus , which is among the most abundant and prevalent species in the human gut .', 'These properties ensure that the B . vulgatus genome has high coverage in many samples , which enables more precise estimates of the allele frequencies in each sample ( Fig 1A–1D ) .', 'The overall levels of within-host diversity for this species are summarized in Fig 1E , based on the fraction of synonymous sites in core genes with intermediate allele frequencies ( white region in Fig 1A–1D ) .', 'This measure of within-host genetic variation varies widely across the samples: some metagenomes have only a few variants along the B . vulgatus genome , while others have mutations at more than 1% of all synonymous sites ( comparable to the differences between samples , S5 Fig ) .', 'Similar patterns are observed in many other prevalent species ( S3 Fig ) .', 'We first asked whether these patterns are consistent with a model in which each host is colonized by a single B . vulgatus clone , so that the intermediate frequency variants represent mutations that have arisen since colonization .', 'Using conservatively high estimates for per-site mutation rates ( μ~10−9 [47] ) , generation times ( approximately 10 per day [48] ) , and time since colonization ( <100 years ) , this model predicts that the neutral polymorphism rate at synonymous sites should be no greater than 0 . 1% ( S1B Text , part', 'ii ) .', 'This is at odds with the higher levels of diversity observed in many samples ( Fig 1E and S3 Fig ) .', 'Instead , we conclude that the samples with higher synonymous diversity have been colonized by multiple divergent bacterial lineages that accumulated mutations for many generations before coming together in the same gut community .', 'As a plausible alternative , we next asked whether the data are consistent with a large number of colonizing lineages ( nc≫1 ) drawn at random from the broader population .', 'However , this process is expected to produce fairly consistent polymorphism rates and allele frequency distributions in different samples , which is at odds with the variability we observe even among the high-diversity samples ( e . g . , Fig 1A , 1B , S1 Fig and S2 Fig ) .', 'Instead , we hypothesize that many of the high-diversity hosts have been colonized by just a few diverged lineages [i . e . , ( nc−1 ) ∼O ( 1 ) ] .', 'Consistent with this hypothesis , the distribution of allele frequencies in each host is often strongly peaked around a few characteristic frequencies , suggesting a mixture of several distinct lineages ( Fig 1A–1C , S1 Fig and S2 Fig ) .', 'Similar findings have recently been reported in a number of other host-associated microbes , including several species of gut bacteria [4 , 35 , 49 , 50] .', 'Fig 1A–1C shows that hosts can vary both in the apparent number of colonizing lineages and the frequencies at which they are mixed together .', 'As a result , we cannot exclude the possibility that even the low-diversity samples ( e . g . , Fig 1D ) are colonized by multiple lineages that happen to fall below the detection threshold set by the depth of sequencing .', 'Compared with the extreme cases of single-colonization ( nc = 1 ) or colonization by many strains ( nc≫1 ) , it is more difficult to identify evolutionary changes between lineages when there are only few strains at intermediate frequency .', 'In this scenario , within-host populations are not clonal , but the corresponding allele frequencies derive from idiosyncratic colonization processes rather than a large random sample from the population ( as , e . g . , in [16] ) .', 'To disentangle genetic changes between lineages from these host-specific factors , we must estimate phased haplotypes ( or "strains" ) from the distribution of allele frequencies within individual hosts .', 'This is a complicated inverse problem , and we will not attempt to solve the general case here .', 'Instead , we adopt an approach similar to [35] and others , and leverage the fact that the lineage structure in certain hosts is sufficiently simple that we can assign alleles to the dominant lineage with a high degree of confidence .', 'Our approach is based on the simple observation that two high-frequency variants must co-occur in an appreciable fraction of cells ( S1C Text , part', 'i ) .', 'This "pigeonhole principle" suggests that we can estimate the genotype of one of the lineages in a mixed sample by taking the major alleles present above some threshold frequency , f*≫50% , and treating the remaining sites as missing data .', 'Although the potential errors increase with the length of the inferred haplotype , we will not actually require genome-length haplotypes for our analysis here .', 'Instead , we leverage the fact that significant evolutionary information is already encoded in the marginal distributions of one- and two-site haplotypes , so that these "quasi-phased" lineages will be sufficient for our present purposes .', 'The major challenge with this approach is that we do not observe the true allele frequency directly but must instead estimate it from a noisy sample of sequencing reads .', 'This can lead to phasing errors when the true major allele is sampled at low frequency by chance and is assigned to the opposite lineage ( S4 Fig ) .', 'We will refer to these as "polarization errors , " because they stem from an incorrect inference of the major allele .', 'The probability of a polarization error will vary dramatically depending on the sequencing coverage and the true frequency of the major allele ( S1C Text , part', 'ii ) .', 'Previous approaches based on consensus alleles [35 , 37] can therefore induce an unknown number of errors that make it difficult to confidently detect a small number of evolutionary changes between samples .', 'In S1C Text , we show that by explicitly modeling the sampling error process , the expected probability of a polarization error in our cohort can be bounded to be sufficiently low if we take f* = 80% , and if we restrict our attention to samples with sufficiently high coverage and sufficiently low rates of intermediate-frequency polymorphism .', 'We will refer to these as quasi-phaseable ( QP ) samples .', 'In the B . vulgatus example above , Fig 1C and 1D are classified as QP , while Fig 1A and 1B are not .', 'Note that quasi-phaseability is separately defined for each species in a metagenomic sample , rather than for the sample as a whole .', 'For simplicity , we will still refer to these species-sample combinations as QP samples , with the implicit understanding that they refer to a particular focal species .', 'In Fig 1F , we plot the distribution of QP samples across the most prevalent gut bacterial species in our panel .', 'The fraction of QP samples varies between species , ranging from about 50% in the case of Prevotella copri to nearly 100% for B . fragilis [4] , and it accounts for much of the variation in the average polymorphism rate between species ( S6 Fig ) .', 'Most individuals carry a mixture of QP and non-QP species ( S7 Fig ) , suggesting that quasi-phaseability arises independently for each species in a sample , rather than for the sample as a whole .', 'Thus , although many species-sample combinations are not QP , our approximately 500-sample cohort still contains tens to hundreds of QP samples in many prevalent species , yielding about 3 , 000 quasi-phased haplotypes in total .', 'Consistent with previous studies of the stability of personal microbiomes [31 , 35 , 51] , a majority of the longitudinally sampled species maintain their QP classification at both time points , although this pattern is not universal ( S8 Fig ) .', 'We will revisit the peculiar properties of this within-host lineage distribution in “Discussion . ”', 'For the remainder of the analysis , we will take the distribution in Fig 1F as given and focus on leveraging the QP samples to quantify the evolutionary changes that accumulate between lineages in different samples .', 'We investigate two types of evolutionary changes between lineages in different QP samples .', 'The first class consists of single nucleotide differences , which are defined as SNVs that segregate at frequencies ≤1−f* in one sample and ≥f* in another , with f*≈80% as above ( S4 Fig ) .', 'These thresholds are chosen to ensure a low genome-wide false positive rate given the typical coverage and allele frequency distributions among the QP samples in our panel ( S1C Text , part', 'iv ) .', 'The second class consists of differences in gene presence or absence , in which the relative copy number of a gene , c , is below the threshold of detection ( c<0 . 05 ) in one sample and is consistent with a single-copy gene ( 0 . 6<c<1 . 2 , see S9 Fig ) in the other sample .', 'These thresholds are chosen to ensure a low genome-wide false positive rate across the QP samples , given the typical variation in sequencing coverage along the genome ( S1C Text , part', 'v ) , and to minimize mapping artifacts ( S1A Text , part', 'ii ) .', 'Note that these SNV and gene changes represent only a subset of the potential differences between lineages .', 'We neglect other evolutionary changes ( e . g . , indels , genome rearrangements , or changes in high copy number genes ) that are more difficult to quantify in a metagenomic sample , as well as more subtle changes in allele frequency and gene copy number that do not reach our stringent detection thresholds .', 'We will revisit these and other limitations in more detail in “Discussion” .'], ['By focusing on the QP samples for each species , we can measure genetic differences between lineages in different hosts , as well as within hosts over short time periods .', 'Descriptive summaries of this variation have been reported elsewhere [31 , 33–35 , 37 , 44] .', 'Here , we aim to leverage these patterns ( and the increased resolution of the QP samples ) to quantify the evolutionary dynamics that operate within species of gut bacteria , both within and across hosts .', 'To interpret within-host changes in an evolutionary context , it will be useful to first understand the structure of genetic variation between lineages in different hosts .', 'This variation reflects the long-term population genetic forces that operate within each species , presumably integrating over many rounds of colonization , growth , and dispersal .', 'To investigate these forces , we first analyzed the average nucleotide divergence between strains of a given species in different pairs of QP hosts ( Fig 2A ) .', 'In the case of twins , we included only a single host from each pair , to better approximate a random sample from the population .', 'Fig 2B shows the distribution of pairwise divergence , averaged across the core genome , for about 40 of the most prevalent bacterial species in our cohort .', 'In a panmictic , neutrally evolving population , we would expect these distances to be clustered around their average value , d≈2μTc , where Tc is the coalescent timescale for the across-host population [52] .', 'By contrast , Fig 2 shows striking differences in the degree of relatedness for strains in different hosts .', 'Even at this coarse , core-genome-wide level , the genetic distances vary over several orders of magnitude .', 'Some species show multiple peaks of divergence for high values of d , consistent with the presence of subspecies [36] , ecotypes [53 , 54] , or other strong forms of population structure .', 'These coarse groupings have been observed previously and are not our primary focus here .', 'Rather , we seek to understand the population genetic forces that operate at finer levels of taxonomic resolution .', 'From this perspective , the more surprising parts of Fig 2 are the thousands of pairs of lineages with extremely low between-host divergence ( e . g . , d≲0 . 01% ) , more than an order of magnitude below the median values in most species .', 'Similar observations have recently been reported by [35] and are often interpreted as strain sharing across hosts .', 'However , the evolutionary interpretation of these closely related strains remains unclear .', 'The simplest explanation for a long tail of closely related strains is cryptic relatedness [55] , arising from a breakdown of random sampling .', 'For microbes , this can occur when two cells are sampled from the same clonal expansion , e . g . , when strains are transferred between mothers and infants [33 , 56] , between cohabitating individuals [46] , or within a hospital outbreak [57] .', 'While these transmission events have been observed in other studies , they are unlikely to account for the patterns here .', 'All of the lineages in Fig 2 are sampled from individuals in different households , and more than a third of the closely related pairs derive from individuals on different continents ( Fig 2B ) .', 'Of course , there could still be some other geographic variable , beyond household or continent of origin , that could explain an elevated probability of transmission between two individuals .', 'Fortunately , our metagenomic approach allows us to rule out these additional sources of cryptic host relatedness by leveraging multiple species comparisons for the same pair of hosts .', 'If there were a hidden geographic variable , then we would expect that individuals with closely related strains in one species would be much more likely to share closely related strains in other species as well .', 'However , we observe only a small fraction of hosts that share multiple closely related strains ( Fig 2C ) , consistent with a null model in which these strains are randomly and independently distributed across hosts .', 'This suggests that host-wide sampling biases are not the primary driver of the closely related strains in Fig 2 .', 'Although the rates of nucleotide divergence are low , the vast majority of these strains are still genetically distinguishable from each other .', 'The absolute number of SNV differences typically exceeds our estimated false positive rate ( S10A Fig , S1C Text , part iv ) , and these SNV differences are often accompanied by ≳10 differences in gene content ( S10B Fig ) .', 'Furthermore , we found that closely related strains frequently differed in their collections of private marker SNVs ( S11 Fig ) , which are often used to track strain transmission events [33 , 46] .', 'Together , these lines of evidence suggest that closely related strains are often genetically distinct and do not arise from a simple clonal expansion .', 'Instead , the data suggest that there are additional population genetic timescales beyond Tc that are relevant for microbial evolution .', 'This hypothesis is bolstered by the large number of species , particularly in the Bacteroides genus , with anomalously low divergence rates between some pairs of hosts .', 'However , we note that this pattern is not universal: some genera , like Alistipes or Eubacterium , show more uniform rates of divergence between hosts .', 'Apart from these phylogenetic correlations , we cannot yet explain why some species have low-divergence host pairs and others do not .', 'Natural candidates such as sample size , abundance , vertical transmissibility [33] , or sporulation score [58] struggle to explain the differences between Bacteroides and Alistipes species .', 'We next examined how natural selection influences the genetic diversity observed between hosts .', 'Previous work has suggested that genetic diversity in many species of gut bacteria is strongly constrained by purifying selection , which purges deleterious mutations that accumulate between hosts [31] .', 'However , the temporal dynamics of this process remain poorly understood .', 'We do not know whether purifying selection acts quickly enough to prevent deleterious mutations from spreading to other hosts , or if deleterious mutations typically spread across multiple hosts before they are purged .', 'In addition , it is plausible that the dominant mode of natural selection could be different for the closely related strains above ( e . g . , if they reflect recent ecological diversification [15] ) .', 'To address these questions , we analyzed the relative contribution of synonymous and nonsynonymous mutations that comprise the overall divergence rates in Fig 2A .', 'We focused on the ratio between the per-site divergence at nonsynonymous sites ( dN ) and the corresponding value at synonymous sites ( dS ) .', 'Under the assumption that synonymous mutations are effectively neutral , the ratio dN/dS measures the average action of natural selection on mutations at nonsynonymous sites .', 'In Fig 3 , we plot these dN/dS estimates across every pair of QP hosts for each of the prevalent species in Fig 2A .', 'The values of dN/dS are plotted as a function of dS , which serves as a proxy for the average divergence time across the genome .', 'We observe a consistent negative relationship between these two quantities across the prevalent species in Fig 2 .', 'For large divergence times ( dS~1% ) , we observe only a small fraction of nonsynonymous mutations ( dN/dS~0 . 1 ) , indicating widespread purifying selection on amino acid replacements [31] .', 'Yet , among more closely related strains , we observe a much higher fraction of nonsynonymous changes , with dN/dS approaching unity when dS~0 . 01% ( we observe a similar trend if we restrict our attention to singleton SNVs , S12 Fig ) .', 'Moreover , this negative relationship between dN/dS and dS is much more pronounced than the between-species variation in the typical values of dN/dS ( black crosses in Fig 3 ) .', 'While between-species variation may be driven by mutational biases , the strong within-species signal indicates that there are consistent differences in the action of natural selection as a function of time .', 'In principle , the dN/dS increases in the recent past could be driven by interesting biological processes , such as enhanced adaptation or ecological diversification on short timescales , or a recent global shift in selection pressures caused by host-specific factors ( e . g . , the introduction of agriculture ) .', 'However , the data in Fig 3 appear to be well explained by an even simpler null model of purifying selection , in which deleterious mutations are purged over a timescale inversely proportional to their cost ( S1D Text ) .', 'This dynamical model can explain the varying signatures of natural selection without requiring that the selective pressures themselves vary over time .', 'We find reasonable quantitative agreement for a simple distribution of fitness effects , in which 10% of nonsynonymous sites are neutral and the remaining 90% have fitness costs on the order of s/μ~105 .', 'Although the true model is likely more complicated , we argue that this simple null model should be excluded before more elaborate explanations are considered .', 'For example , unambiguous proof of recent adaptation could be observed if dN/dS consistently exceeded 1 among the most closely related strains ( because this can only occur by chance under purifying selection ) .', 'While a few of the individual comparisons in Fig 3A have dN/dS>1 , the cumulative version in Fig 3B shows that dN/dS does not significantly exceed 1 , even for the lowest values of dS .', 'This suggests that , if positive selection is present , it is not sufficiently widespread to overpower the signal of purifying selection in these global dN/dS measurements .', 'However , there is also substantial variation around the average trend in Fig 3 , which could hide important biological variation among species ( or among different genomic regions in the same species ) .', 'Resolving the signatures of natural selection at these finer scales remains an important avenue for future work .', 'So far , we have focused on evolutionary changes that accumulate over many host colonization cycles .', 'In principle , evolutionary changes can also accumulate within hosts over time .', 'Longitudinal studies have shown that strains and metagenomes sampled from the same host are more similar to each other on average than to samples from different hosts [31 , 33 , 35 , 44 , 64 , 65] .', 'This suggests that resident populations of bacteria persist within hosts for at least a year ( approximately 300 to 3 , 000 generations ) , which is potentially enough time for evolutionary adaptation to occur [7] .', 'However , the limited resolution of previous polymorphism- [31] or consensus-based comparisons [35 , 44] has made it difficult to quantify the individual changes that accumulate within hosts and to interpret these changes in an evolutionary context .'], ['Evolutionary processes can play an important role in many microbial communities .', 'Yet , despite increasing amounts of sequence data , our understanding of these processes is often limited by our ability to resolve evolutionary changes in populations from complex communities .', 'In this work , we quantify the evolutionary forces that operate within bacteria in the human gut microbiome by characterizing in detail the lineage structure of approximately 40 species in metagenomic samples from individual hosts .', 'Building on previous work [35] and others , we found that many resident populations from a variety of prevalent species are best described by an "oligo-colonization" model , in which a few distinct strains from the larger population are present at intermediate frequencies , with the identities and frequencies of these strains varying from person to person ( Fig 1 ) .', 'The distribution of strain frequencies in this oligo-colonization model is itself quite interesting: in the absence of fine tuning , it is not clear what mechanisms would allow for a second or third strain to reach intermediate frequency , while preventing a large number of other lineages from entering and growing to detectable levels at the same time .', 'A better understanding of the colonization process and how it might vary among the species in Fig 1F is an important avenue for future work .', 'Given the wide variation among species and hosts , we chose to focus on a subset of samples with particularly simple strain mixtures for a given species , in which we can resolve evolutionary changes in the dominant lineage with a high degree of confidence .', 'Our quasi-phasing approach can be viewed as a refinement of the consensus approximation employed in earlier studies [4 , 35 , 37 , 38] but with more quantitative estimates of the errors associated with detecting genetic differences between lineages in different samples .', 'By analyzing genetic differences between lineages in separate hosts , we found that long-term evolutionary dynamics in many gut bacteria are consistent with quasi-sexual evolution and purifying selection , with relatively weak geographic structure .', 'Earlier work had documented extensive horizontal transfer between distantly related species in the gut [71 , 72] , but our ability to estimate rates of recombination within species was previously limited by the small number of sequenced isolates for many species of gut bacteria [73] .', 'The high rates of homologous recombination we observed with our quasi-phasing approach are qualitatively consistent with previous observations in other bacterial species [16 , 73–77]; although the rates of recombination are high relative to the typical divergence time , we note that they may still allow for genome-wide sweeps or divergence between nascent ecotypes given sufficiently strong selection pressures .', 'Beyond t
['Introduction', 'Materials and methods', 'Results', 'Discussion']
['Gut microbiota are shaped by a combination of ecological and evolutionary forces .', 'While the ecological dynamics have been extensively studied , much less is known about how species of gut bacteria evolve over time .', 'Here , we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples .', 'We use this approach to study evolution in approximately 40 prevalent species in the human gut .', 'Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales , we identify new genealogical signatures that challenge standard population genetic models of these processes .', 'Within hosts , we find that genetic differences that accumulate over 6-month timescales are only rarely attributable to replacement by distantly related strains .', 'Instead , the resident strains more commonly acquire a smaller number of putative evolutionary changes , in which nucleotide variants or gene gains or losses rapidly sweep to high frequency .', 'By comparing these mutations with the typical between-host differences , we find evidence that some sweeps may be seeded by recombination , in addition to new mutations .', 'However , comparisons of adult twins suggest that replacement eventually overwhelms evolution over multi-decade timescales , hinting at fundamental limits to the extent of local adaptation .', 'Together , our results suggest that gut bacteria can evolve on human-relevant timescales , and they highlight the connections between these short-term evolutionary dynamics and longer-term evolution across hosts .']
['The human gut harbors a diverse microbial community whose composition is shaped by a variety of ecological forces .', 'Given the high rates of turnover , the residents of this community might also have the opportunity to evolve over time by acquiring heritable changes to their genomes .', 'Yet , despite the potential importance of these effects , we currently know very little about the evolutionary dynamics that occur within species in this complex community .', 'Here , we introduce a new approach for extracting evolutionary signals from a large panel of human gut metagenomes and for interpreting these signals using simple null models from population genetics .', 'We use this approach to quantify the evolutionary dynamics of approximately 40 prevalent species of gut bacteria , both within individual hosts and across the larger population .', 'We find that resident populations of gut bacteria can evolve within their hosts on short timescales , but after many years , the resident populations are typically replaced by distantly related strains .', 'The patterns of variation across hosts indicate widespread recombination within species , but the quantitative signals suggest interesting departures from traditional population genetic models .', 'Together , these results show that short-term evolution in the gut microbiome may be more complex and widespread than is often assumed .']
['bacteriology', 'organismal evolution', 'gut bacteria', 'population genetics', 'microbiology', 'twins', 'developmental biology', 'metagenomics', 'microbial evolution', 'evolutionary adaptation', 'population biology', 'bacteria', 'evolutionary genetics', 'genetics', 'biology and life sciences', 'genomics', 'evolutionary biology', 'bacterial evolution', 'evolutionary processes', 'organisms']
A population genetic analysis of human gut metagenomes reveals short-term evolution within individual species of gut bacteria, both within individual hosts, and across the larger population.