Population Genetics in the Human Microbiome
Authors: Nandita R. Garud, Katherine S. Pollard
Journal: Trends in Genetics (2019)

Genetic variation in host-associated microbiomes can be assayed in a high-throughput manner with a variety of technologies.Many bacterial species recombine extensively, although they asexually reproduce.The genetic diversity of many species within and across hosts is spatially structured.Evidence for rapid adaptation within hosts is starting to emerge.Modeling efforts are connecting microbiome genetic variants with host phenotypes, highlighting the biomedical importance of genetic variation in the microbiome. While the human microbiome's structure and function have been extensively studied, its within-species genetic diversity is less well understood. However, genetic mutations in the microbiome can confer biomedically relevant traits, such as the ability to extract nutrients from food, metabolize drugs, evade antibiotics, and communicate with the host immune system. The population genetic processes by which these traits evolve are complex, in part due to interacting ecological and evolutionary forces in the microbiome. Advances in metagenomic sequencing, coupled with bioinformatics tools and population genetic models, facilitate quantification of microbiome genetic variation and inferences about how this diversity arises, evolves, and correlates with traits of both microbes and hosts. In this review, we explore the population genetic forces (mutation, recombination, drift, and selection) that shape microbiome genetic diversity within and between hosts, as well as efforts towards predictive models that leverage microbiome genetics. While the human microbiome's structure and function have been extensively studied, its within-species genetic diversity is less well understood. However, genetic mutations in the microbiome can confer biomedically relevant traits, such as the ability to extract nutrients from food, metabolize drugs, evade antibiotics, and communicate with the host immune system. The population genetic processes by which these traits evolve are complex, in part due to interacting ecological and evolutionary forces in the microbiome. Advances in metagenomic sequencing, coupled with bioinformatics tools and population genetic models, facilitate quantification of microbiome genetic variation and inferences about how this diversity arises, evolves, and correlates with traits of both microbes and hosts. In this review, we explore the population genetic forces (mutation, recombination, drift, and selection) that shape microbiome genetic diversity within and between hosts, as well as efforts towards predictive models that leverage microbiome genetics. The human microbiome comprises bacteria, archaea, viruses, and microbial eukaryotes living in our bodies. The taxonomic composition of these communities has been extensively studied and is significantly associated with a variety of diseases and traits [1Cho I. Blaser M.J. The human microbiome: at the interface of health and disease.Nat. Rev. Genet. 2012; 13: 260-270Crossref PubMed Scopus (1234) Google Scholar]. However, each species in the microbiome is genetically heterogeneous, comprising individual cells whose genomes contain different mutations [2Schloissnig S. et al.Genomic variation landscape of the human gut microbiome.Nature. 2013; 493: 45-50Crossref PubMed Scopus (362) Google Scholar]. Widespread deployment of sequencing technologies (Box 1) has revealed that most microbiota harbor extensive genetic variation between hosts, within a host over time, and even within a host at a given time [2Schloissnig S. et al.Genomic variation landscape of the human gut microbiome.Nature. 2013; 493: 45-50Crossref PubMed Scopus (362) Google Scholar,3Faith J.J. et al.The long-term stability of the human gut microbiota.Science. 2013; 341: 1237439Crossref PubMed Scopus (726) Google Scholar]. As in other species, this variation comprises single-nucleotide variants (SNVs) [2Schloissnig S. et al.Genomic variation landscape of the human gut microbiome.Nature. 2013; 493: 45-50Crossref PubMed Scopus (362) Google Scholar], short insertions and deletions (indels) [4Chen J.Q. et al.Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria.Mol. Biol. Evol. 2009; 26: 1523-1531Crossref PubMed Scopus (0) Google Scholar], and larger structural variants (SVs) [5Zeevi D. et al.Structural variation in the gut microbiome associates with host health.Nature. 2019; 568: 43-48Crossref PubMed Scopus (14) Google Scholar], which include duplications, deletions, insertions, and inversions and can generate gene copy-number variants (CNVs) [6Greenblum S. et al.Extensive strain-level copy-number variation across human gut microbiome species.Cell. 2015; 160: 583-594Abstract Full Text Full Text PDF PubMed Scopus (97) Google Scholar]. There has been substantial progress towards quantifying genetic diversity in the human microbiome [2Schloissnig S. et al.Genomic variation landscape of the human gut microbiome.Nature. 2013; 493: 45-50Crossref PubMed Scopus (362) Google Scholar,6Greenblum S. et al.Extensive strain-level copy-number variation across human gut microbiome species.Cell. 2015; 160: 583-594Abstract Full Text Full Text PDF PubMed Scopus (97) Google Scholar, 7Nayfach S. et al.An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.Genome Res. 2016; 26: 1612-1625Crossref PubMed Scopus (84) Google Scholar, 8Scholz M. et al.Strain-level microbial epidemiology and population genomics from shotgun metagenomics.Nat. Methods. 2016; 13: 435-438Crossref PubMed Scopus (106) Google Scholar].Box 1How Do We Obtain the Necessary Genomic Information to Study Population Genetics in the Microbiome?Genetic variants in the microbiome are assayed using a variety of approaches that vary on several dimensions including whether they require culturing, the number of species sampled concurrently, the length of the resulting haplotypes and reads, and cost.Cultured Isolate SequencingMuch of microbiome population genetics relies on identifying SNVs or SVs among sequenced and assembled genomes from cultured isolates. Since variants are linked in assembled genomes, studies of recombination, HGT, and nucleotide changes associated with evolution are feasible [34Zhao S. et al.Adaptive evolution within gut microbiomes of healthy people.Cell Host Microbe. 2019; 25: 656-667Abstract Full Text Full Text PDF PubMed Scopus (13) Google Scholar,35Ghalayini M. et al.Evolution of a dominant natural isolate of Escherichia coli in the human gut over the course of a year suggests a neutral evolution with reduced effective population size.Appl. Environ. Microbiol. 2018; 84 (e02377-17)Crossref PubMed Scopus (6) Google Scholar,76Smith J.M. et al.How clonal are bacteria?.Proc. Natl Acad. Sci. U. S. A. 1993; 90: 4384-4388Crossref PubMed Google Scholar,117Barroso-Batista J. et al.The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps.PLoS Genet. 2014; 10: e1004182Crossref PubMed Scopus (61) Google Scholar,127Karami N. et al.Transfer of an ampicillin resistance gene between two Escherichia coli strains in the bowel microbiota of an infant treated with antibiotics.J. Antimicrob. Chemother. 2007; 60: 1142-1145Crossref PubMed Scopus (61) Google Scholar,149Gumpert H. et al.Transfer and persistence of a multi-drug resistance plasmid in situ of the infant gut microbiota in the absence of antibiotic treatment.Front. Microbiol. 2017; 8: 1852Crossref PubMed Scopus (11) Google Scholar,152Lescat M. et al.Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut.Mol. Ecol. 2017; 26: 1802-1817Crossref PubMed Scopus (19) Google Scholar]. Throughput and difficult-to-culture species are limitations, but targeted culturing efforts [58Browne H.P. et al.Culturing of "unculturable" human microbiota reveals novel taxa and extensive sporulation.Nature. 2016; 533: 543-546Crossref PubMed Google Scholar,153Lagier J.C. et al.Microbial culturomics: paradigm shift in the human gut microbiome study.Clin. Microbiol. Infect. 2012; 18: 1185-1193Abstract Full Text Full Text PDF PubMed Scopus (531) Google Scholar, 154Forster S.C. et al.A human gut bacterial genome and culture collection for improved metagenomic analyses.Nat. Biotechnol. 2019; 37: 186-192Crossref PubMed Scopus (29) Google Scholar, 155Zou Y. et al.1,520 Reference genomes from cultivated human gut bacteria enable functional microbiome analyses.Nat. Biotechnol. 2019; 37: 179-185Crossref PubMed Scopus (29) Google Scholar, 156Poyet M. et al.A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research.Nat. Med. 2019; 25: 1442-1452Crossref PubMed Scopus (1) Google Scholar], multiplexed sequencing [34Zhao S. et al.Adaptive evolution within gut microbiomes of healthy people.Cell Host Microbe. 2019; 25: 656-667Abstract Full Text Full Text PDF PubMed Scopus (13) Google Scholar], and microfluidics [157Ma L. et al.Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa.Proc. Natl Acad. Sci. U. S. A. 2014; 111: 9768-9773Crossref PubMed Scopus (60) Google Scholar] are helping [158Nelson K.E. et al.A catalog of reference genomes from the human microbiome.Science. 2010; 328: 994-999Crossref PubMed Scopus (411) Google Scholar].MetagenotypingShotgun metagenomics is the sequencing of pooled DNA from microbial communities. By aligning reads to genomes (or 'pangenomes' of all genes observed in a species) and applying statistical models, both SNVs and SVs can be called [2Schloissnig S. et al.Genomic variation landscape of the human gut microbiome.Nature. 2013; 493: 45-50Crossref PubMed Scopus (362) Google Scholar,6Greenblum S. et al.Extensive strain-level copy-number variation across human gut microbiome species.Cell. 2015; 160: 583-594Abstract Full Text Full Text PDF PubMed Scopus (97) Google Scholar,7Nayfach S. et al.An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.Genome Res. 2016; 26: 1612-1625Crossref PubMed Scopus (84) Google Scholar,46Truong D.T. et al.Microbial strain-level population structure and genetic diversity from metagenomes.Genome Res. 2017; 27: 626-638Crossref PubMed Scopus (93) Google Scholar,151Smillie C.S. et al.Strain tracking reveals the determinants of bacterial engraftment in the human gut following fecal microbiota transplantation.Cell Host Microbe. 2018; 23: 229-240.e5Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar,159Segata N. et al.Metagenomic microbial community profiling using unique clade-specific marker genes.Nat. Methods. 2012; 9: 811-814Crossref PubMed Scopus (600) Google Scholar]. Metagenotyping is relatively unbiased, does not require culturing, and can be used to study hundreds of species simultaneously for relatively low cost. However, alignment to a database misses novel genes and species, is sensitive to reads that align to multiple species or genes [5Zeevi D. et al.Structural variation in the gut microbiome associates with host health.Nature. 2019; 568: 43-48Crossref PubMed Scopus (14) Google Scholar], and does not provide long-range linkage information, although probabilistic models can be used to computationally phase variants and resolve short-range haplotypes for abundant species [33Garud N.R. et al.Evolutionary dynamics of bacteria in the gut microbiome within and across hosts.PLoS Biol. 2019; 17: e3000102Crossref PubMed Scopus (14) Google Scholar]. Metagenotyping is distinct from methods that quantify gene or pathway abundance across all species from metagenomes [160Franzosa E.A. et al.Species-level functional profiling of metagenomes and metatranscriptomes.Nat. Methods. 2018; 15: 962-968Crossref PubMed Scopus (53) Google Scholar] or use genes with covarying abundance to define metagenomic linkage groups as estimates of species [120Qin J. et al.A metagenome-wide association study of gut microbiota in type 2 diabetes.Nature. 2012; 490: 55-60Crossref PubMed Scopus (2011) Google Scholar,161Alneberg J. et al.Binning metagenomic contigs by coverage and composition.Nat. Methods. 2014; 11: 1144-1146Crossref PubMed Scopus (320) Google Scholar,162Parks D.H. et al.Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.Nat. Microbiol. 2017; 2: 1533-1542Crossref PubMed Scopus (190) Google Scholar].Metagenome-Assembled Genomes (MAGs)Genomes can be recovered from metagenomes de novo using binning and assembly [120Qin J. et al.A metagenome-wide association study of gut microbiota in type 2 diabetes.Nature. 2012; 490: 55-60Crossref PubMed Scopus (2011) Google Scholar,161Alneberg J. et al.Binning metagenomic contigs by coverage and composition.Nat. Methods. 2014; 11: 1144-1146Crossref PubMed Scopus (320) Google Scholar,162Parks D.H. et al.Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.Nat. Microbiol. 2017; 2: 1533-1542Crossref PubMed Scopus (190) Google Scholar], which allows the characterization of new species and variant discovery in both known and novel species [163Nayfach S. et al.New insights from uncultivated genomes of the global human gut microbiome.Nature. 2019; 568: 505-510Crossref PubMed Scopus (17) Google Scholar, 164Pasolli E. et al.Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle.Cell. 2019; 176: 649-662.e20Abstract Full Text Full Text PDF PubMed Scopus (70) Google Scholar, 165Almeida A. et al.A new genomic blueprint of the human gut microbiota.Nature. 2019; 568: 499-504Crossref PubMed Scopus (39) Google Scholar]. MAGs can rapidly expand the number of reference genomes and observed genetic diversity of a species, as for Prevotella copri, which recently went from having one genome to >1000 genomes from four distinct clades [54Tett A. et al.The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernised populations.Cell Host Microbe. 2019; 26 (666–679.e7)Abstract Full Text Full Text PDF Scopus (2) Google Scholar,133De Filippis F. et al.Distinct genetic and functional traits of human intestinal Prevotella copri strains are associated with different habitual diets.Cell Host Microbe. 2019; 25: 444-453.e3Abstract Full Text Full Text PDF PubMed Scopus (14) Google Scholar]. Chimeric and incomplete assemblies are limitations, especially for lower-abundance species. Assembly is improving with chromatin capture scaffolding [166Stewart R.D. et al.Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen.Nat. Commun. 2018; 9: 870Crossref PubMed Scopus (65) Google Scholar] and longer reads. Improved methods for assessing MAG quality and completeness will be helpful.Single-Cell and Read-Cloud SequencingFlow cytometry [167Mou X. et al.Flow-cytometric cell sorting and subsequent molecular analyses for culture-independent identification of bacterioplankton involved in dimethylsulfoniopropionate transformations.Appl. Environ. Microbiol. 2005; 71: 1405-1416Crossref PubMed Scopus (25) Google Scholar] and microfluidics [157Ma L. et al.Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa.Proc. Natl Acad. Sci. U. S. A. 2014; 111: 9768-9773Crossref PubMed Scopus (60) Google Scholar,168Lan F. et al.Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding.Nat. Biotechnol. 2017; 35: 640-646Crossref PubMed Scopus (82) Google Scholar] can be used to capture and barcode single cells, small numbers of cells, or small numbers of DNA fragments [169Bishara A. et al.High-quality genome sequences of uncultured microbes by assembly of read clouds.Nat. Biotechnol. 2018; 36: 1067-1075Crossref Scopus (11) Google Scholar] from a sample without culturing. Coupled with deep sequencing and specialized bioinformatics methods, these techniques assemble genome segments from which genetic variants, including mobile genes [63Brito I.L. et al.Mobile genes in the human microbiome are structured from global to individual scales.Nature. 2016; 535: 435-439Crossref PubMed Scopus (122) Google Scholar], can be identified. This strategy may soon produce genomes comparable with isolates with high throughput and no culture bias. Genetic variants in the microbiome are assayed using a variety of approaches that vary on several dimensions including whether they require culturing, the number of species sampled concurrently, the length of the resulting haplotypes and reads, and cost. Much of microbiome population genetics relies on identifying SNVs or SVs among sequenced and assembled genomes from cultured isolates. Since variants are linked in assembled genomes, studies of recombination, HGT, and nucleotide changes associated with evolution are feasible [34Zhao S. et al.Adaptive evolution within gut microbiomes of healthy people.Cell Host Microbe. 2019; 25: 656-667Abstract Full Text Full Text PDF PubMed Scopus (13) Google Scholar,35Ghalayini M. et al.Evolution of a dominant natural isolate of Escherichia coli in the human gut over the course of a year suggests a neutral evolution with reduced effective population size.Appl. Environ. Microbiol. 2018; 84 (e02377-17)Crossref PubMed Scopus (6) Google Scholar,76Smith J.M. et al.How clonal are bacteria?.Proc. Natl Acad. Sci. U. S. A. 1993; 90: 4384-4388Crossref PubMed Google Scholar,117Barroso-Batista J. et al.The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps.PLoS Genet. 2014; 10: e1004182Crossref PubMed Scopus (61) Google Scholar,127Karami N. et al.Transfer of an ampicillin resistance gene between two Escherichia coli strains in the bowel microbiota of an infant treated with antibiotics.J. Antimicrob. Chemother. 2007; 60: 1142-1145Crossref PubMed Scopus (61) Google Scholar,149Gumpert H. et al.Transfer and persistence of a multi-drug resistance plasmid in situ of the infant gut microbiota in the absence of antibiotic treatment.Front. Microbiol. 2017; 8: 1852Crossref PubMed Scopus (11) Google Scholar,152Lescat M. et al.Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut.Mol. Ecol. 2017; 26: 1802-1817Crossref PubMed Scopus (19) Google Scholar]. Throughput and difficult-to-culture species are limitations, but targeted culturing efforts [58Browne H.P. et al.Culturing of "unculturable" human microbiota reveals novel taxa and extensive sporulation.Nature. 2016; 533: 543-546Crossref PubMed Google Scholar,153Lagier J.C. et al.Microbial culturomics: paradigm shift in the human gut microbiome study.Clin. Microbiol. Infect. 2012; 18: 1185-1193Abstract Full Text Full Text PDF PubMed Scopus (531) Google Scholar, 154Forster S.C. et al.A human gut bacterial genome and culture collection for improved metagenomic analyses.Nat. Biotechnol. 2019; 37: 186-192Crossref PubMed Scopus (29) Google Scholar, 155Zou Y. et al.1,520 Reference genomes from cultivated human gut bacteria enable functional microbiome analyses.Nat. Biotechnol. 2019; 37: 179-185Crossref PubMed Scopus (29) Google Scholar, 156Poyet M. et al.A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research.Nat. Med. 2019; 25: 1442-1452Crossref PubMed Scopus (1) Google Scholar], multiplexed sequencing [34Zhao S. et al.Adaptive evolution within gut microbiomes of healthy people.Cell Host Microbe. 2019; 25: 656-667Abstract Full Text Full Text PDF PubMed Scopus (13) Google Scholar], and microfluidics [157Ma L. et al.Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa.Proc. Natl Acad. Sci. U. S. A. 2014; 111: 9768-9773Crossref PubMed Scopus (60) Google Scholar] are helping [158Nelson K.E. et al.A catalog of reference genomes from the human microbiome.Science. 2010; 328: 994-999Crossref PubMed Scopus (411) Google Scholar]. Shotgun metagenomics is the sequencing of pooled DNA from microbial communities. By aligning reads to genomes (or 'pangenomes' of all genes observed in a species) and applying statistical models, both SNVs and SVs can be called [2Schloissnig S. et al.Genomic variation landscape of the human gut microbiome.Nature. 2013; 493: 45-50Crossref PubMed Scopus (362) Google Scholar,6Greenblum S. et al.Extensive strain-level copy-number variation across human gut microbiome species.Cell. 2015; 160: 583-594Abstract Full Text Full Text PDF PubMed Scopus (97) Google Scholar,7Nayfach S. et al.An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.Genome Res. 2016; 26: 1612-1625Crossref PubMed Scopus (84) Google Scholar,46Truong D.T. et al.Microbial strain-level population structure and genetic diversity from metagenomes.Genome Res. 2017; 27: 626-638Crossref PubMed Scopus (93) Google Scholar,151Smillie C.S. et al.Strain tracking reveals the determinants of bacterial engraftment in the human gut following fecal microbiota transplantation.Cell Host Microbe. 2018; 23: 229-240.e5Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar,159Segata N. et al.Metagenomic microbial community profiling using unique clade-specific marker genes.Nat. Methods. 2012; 9: 811-814Crossref PubMed Scopus (600) Google Scholar]. Metagenotyping is relatively unbiased, does not require culturing, and can be used to study hundreds of species simultaneously for relatively low cost. However, alignment to a database misses novel genes and species, is sensitive to reads that align to multiple species or genes [5Zeevi D. et al.Structural variation in the gut microbiome associates with host health.Nature. 2019; 568: 43-48Crossref PubMed Scopus (14) Google Scholar], and does not provide long-range linkage information, although probabilistic models can be used to computationally phase variants and resolve short-range haplotypes for abundant species [33Garud N.R. et al.Evolutionary dynamics of bacteria in the gut microbiome within and across hosts.PLoS Biol. 2019; 17: e3000102Crossref PubMed Scopus (14) Google Scholar]. Metagenotyping is distinct from methods that quantify gene or pathway abundance across all species from metagenomes [160Franzosa E.A. et al.Species-level functional profiling of metagenomes and metatranscriptomes.Nat. Methods. 2018; 15: 962-968Crossref PubMed Scopus (53) Google Scholar] or use genes with covarying abundance to define metagenomic linkage groups as estimates of species [120Qin J. et al.A metagenome-wide association study of gut microbiota in type 2 diabetes.Nature. 2012; 490: 55-60Crossref PubMed Scopus (2011) Google Scholar,161Alneberg J. et al.Binning metagenomic contigs by coverage and composition.Nat. Methods. 2014; 11: 1144-1146Crossref PubMed Scopus (320) Google Scholar,162Parks D.H. et al.Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.Nat. Microbiol. 2017; 2: 1533-1542Crossref PubMed Scopus (190) Google Scholar]. Genomes can be recovered from metagenomes de novo using binning and assembly [120Qin J. et al.A metagenome-wide association study of gut microbiota in type 2 diabetes.Nature. 2012; 490: 55-60Crossref PubMed Scopus (2011) Google Scholar,161Alneberg J. et al.Binning metagenomic contigs by coverage and composition.Nat. Methods. 2014; 11: 1144-1146Crossref PubMed Scopus (320) Google Scholar,162Parks D.H. et al.Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.Nat. Microbiol. 2017; 2: 1533-1542Crossref PubMed Scopus (190) Google Scholar], which allows the characterization of new species and variant discovery in both known and novel species [163Nayfach S. et al.New insights from uncultivated genomes of the global human gut microbiome.Nature. 2019; 568: 505-510Crossref PubMed Scopus (17) Google Scholar, 164Pasolli E. et al.Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle.Cell. 2019; 176: 649-662.e20Abstract Full Text Full Text PDF PubMed Scopus (70) Google Scholar, 165Almeida A. et al.A new genomic blueprint of the human gut microbiota.Nature. 2019; 568: 499-504Crossref PubMed Scopus (39) Google Scholar]. MAGs can rapidly expand the number of reference genomes and observed genetic diversity of a species, as for Prevotella copri, which recently went from having one genome to >1000 genomes from four distinct clades [54Tett A. et al.The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernised populations.Cell Host Microbe. 2019; 26 (666–679.e7)Abstract Full Text Full Text PDF Scopus (2) Google Scholar,133De Filippis F. et al.Distinct genetic and functional traits of human intestinal Prevotella copri strains are associated with different habitual diets.Cell Host Microbe. 2019; 25: 444-453.e3Abstract Full Text Full Text PDF PubMed Scopus (14) Google Scholar]. Chimeric and incomplete assemblies are limitations, especially for lower-abundance species. Assembly is improving with chromatin capture scaffolding [166Stewart R.D. et al.Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen.Nat. Commun. 2018; 9: 870Crossref PubMed Scopus (65) Google Scholar] and longer reads. Improved methods for assessing MAG quality and completeness will be helpful. Flow cytometry [167Mou X. et al.Flow-cytometric cell sorting and subsequent molecular analyses for culture-independent identification of bacterioplankton involved in dimethylsulfoniopropionate transformations.Appl. Environ. Microbiol. 2005; 71: 1405-1416Crossref PubMed Scopus (25) Google Scholar] and microfluidics [157Ma L. et al.Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa.Proc. Natl Acad. Sci. U. S. A. 2014; 111: 9768-9773Crossref PubMed Scopus (60) Google Scholar,168Lan F. et al.Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding.Nat. Biotechnol. 2017; 35: 640-646Crossref PubMed Scopus (82) Google Scholar] can be used to capture and barcode single cells, small numbers of cells, or small numbers of DNA fragments [169Bishara A. et al.High-quality genome sequences of uncultured microbes by assembly of read clouds.Nat. Biotechnol. 2018; 36: 1067-1075Crossref Scopus (11) Google Scholar] from a sample without culturing. Coupled with deep sequencing and specialized bioinformatics methods, these techniques assemble genome segments from which genetic variants, including mobile genes [63Brito I.L. et al.Mobile genes in the human microbiome are structured from global to individual scales.Nature. 2016; 535: 435-439Crossref PubMed Scopus (122) Google Scholar], can be identified. This strategy may soon produce genomes comparable with isolates with high throughput and no culture bias. By contrast, our knowledge of population genetic processes that shape the human microbiome is nascent. Population genetics is a discipline that makes statistical inferences about the evolutionary events that gave rise to patterns of genetic variation across individuals of the same species. The main processes that determine the fate of a new mutation are drift (see Glossary), selection, migration (or transmission), and recombination [9Gillespie J.H. Population Genetics: A Concise Guide. Johns Hopkins University Press, 2004Crossref Google Scholar]. These processes govern how new traits arise and spread among microbes, such as antibiotic resistance [10Jernberg C. et al.Long-term impacts of antibiotic exposure on the human intestinal microbiota.Microbiology. 2010; 156: 3216-3223Crossref PubMed Scopus (466) Google Scholar], drug side effects [11Maurice C.F. et al.Xenobiotics shape the physiology and gene expression of the active human gut microbiome.Cell. 2013; 152: 39-50Abstract Full Text Full Text PDF PubMed Scopus (375) Google Scholar], pathogenic biofilm formation [12Lohse M.B. et al.Development and regulation of single-and multi-species Candida albicans biofilms.Nat. Rev. Microbiol. 2018; 16: 19-31Crossref PubMed Scopus (0) Google Scholar], and responses to diet, sanitation, and health status [13Spanogiannopoulos P. et al.The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism.Nat. Rev. Microbiol. 2016; 14: 273-287Crossref PubMed Scopus (176) Google Scholar]. However, the relative contributions of these forces to microbiome diversity – as well as how they fluctuate over time and across microbiota, genes, and hosts with different phenotypes – remain to be fully understood. A population genetic view of the microbiome provides the opportunity to discover the genetic contribution to traits within microbial populations and to infer the processes creating and maintaining trait-associated genotypes. In this review, we focus on the population genetics of human-associated species, but note lessons learned from other environments. Much of the data discussed are from observational studies of natural populations, but we also discuss experimental methods (Box 2) and the use of model systems to establish causality and to interpret inferences from observational studies of human-associated communities.Box 2In Vitro Experimental Tools for Microbiome Population GeneticsExperimental EvolutionObserving microbes evolve in the laboratory is a useful method to test hypotheses about microbial population genetics in controlled settings. Longitudinal studies of cultured microbes under different conditions, typically starting from one or a few strains, have shown rapid adaptation from both de no