{"id":190424,"date":"2025-12-18T18:52:29","date_gmt":"2025-12-18T18:52:29","guid":{"rendered":"https:\/\/www.newsbeep.com\/nz\/190424\/"},"modified":"2025-12-18T18:52:29","modified_gmt":"2025-12-18T18:52:29","slug":"gene-specific-selective-sweeps-are-pervasive-across-human-gut-microbiomes","status":"publish","type":"post","link":"https:\/\/www.newsbeep.com\/nz\/190424\/","title":{"rendered":"Gene-specific selective sweeps are pervasive across human gut microbiomes"},"content":{"rendered":"<p class=\"c-article-references__text\" id=\"ref-CR1\">Garud, N. R., Good, B. H., Hallatschek, O. &amp; Pollard, K. S. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol. 17, e3000102 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1371\/journal.pbio.3000102\" data-track-item_id=\"10.1371\/journal.pbio.3000102\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1371%2Fjournal.pbio.3000102\" aria-label=\"Article reference 1\" data-doi=\"10.1371\/journal.pbio.3000102\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=30673701\" aria-label=\"PubMed reference 1\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6361464\" aria-label=\"PubMed Central reference 1\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 1\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Evolutionary%20dynamics%20of%20bacteria%20in%20the%20gut%20microbiome%20within%20and%20across%20hosts&amp;journal=PLoS%20Biol.&amp;doi=10.1371%2Fjournal.pbio.3000102&amp;volume=17&amp;publication_year=2019&amp;author=Garud%2CNR&amp;author=Good%2CBH&amp;author=Hallatschek%2CO&amp;author=Pollard%2CKS\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR2\">Zhao, S. et al. Adaptive evolution within gut microbiomes of healthy people. Cell Host Microbe 25, 656\u2013667 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.chom.2019.03.007\" data-track-item_id=\"10.1016\/j.chom.2019.03.007\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.chom.2019.03.007\" aria-label=\"Article reference 2\" data-doi=\"10.1016\/j.chom.2019.03.007\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXotVKgur8%3D\" aria-label=\"CAS reference 2\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=31028005\" aria-label=\"PubMed reference 2\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6749991\" aria-label=\"PubMed Central reference 2\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 2\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Adaptive%20evolution%20within%20gut%20microbiomes%20of%20healthy%20people&amp;journal=Cell%20Host%20Microbe&amp;doi=10.1016%2Fj.chom.2019.03.007&amp;volume=25&amp;pages=656-667&amp;publication_year=2019&amp;author=Zhao%2CS\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR3\">Poyet, M. et al. A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research. Nat. Med. 25, 1442\u20131452 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41591-019-0559-3\" data-track-item_id=\"10.1038\/s41591-019-0559-3\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41591-019-0559-3\" aria-label=\"Article reference 3\" data-doi=\"10.1038\/s41591-019-0559-3\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXhs12gurrP\" aria-label=\"CAS reference 3\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=31477907\" aria-label=\"PubMed reference 3\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 3\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20library%20of%20human%20gut%20bacterial%20isolates%20paired%20with%20longitudinal%20multiomics%20data%20enables%20mechanistic%20microbiome%20research&amp;journal=Nat.%20Med.&amp;doi=10.1038%2Fs41591-019-0559-3&amp;volume=25&amp;pages=1442-1452&amp;publication_year=2019&amp;author=Poyet%2CM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR4\">Yaffe, E. &amp; Relman, D. A. Tracking microbial evolution in the human gut using hi-c reveals extensive horizontal gene transfer, persistence and adaptation. Nat. Microbiol. 5, 343\u2013353 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41564-019-0625-0\" data-track-item_id=\"10.1038\/s41564-019-0625-0\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41564-019-0625-0\" aria-label=\"Article reference 4\" data-doi=\"10.1038\/s41564-019-0625-0\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXjvF2hsQ%3D%3D\" aria-label=\"CAS reference 4\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=31873203\" aria-label=\"PubMed reference 4\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 4\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Tracking%20microbial%20evolution%20in%20the%20human%20gut%20using%20hi-c%20reveals%20extensive%20horizontal%20gene%20transfer%2C%20persistence%20and%20adaptation&amp;journal=Nat.%20Microbiol.&amp;doi=10.1038%2Fs41564-019-0625-0&amp;volume=5&amp;pages=343-353&amp;publication_year=2020&amp;author=Yaffe%2CE&amp;author=Relman%2CDA\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR5\">Zlitni, S. et al. Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale. Genome Med. 12, 50 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener nofollow\" data-track-label=\"10.1186\/s13073-020-00747-0\" data-track-item_id=\"10.1186\/s13073-020-00747-0\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1186\/s13073-020-00747-0\" aria-label=\"Article reference 5\" data-doi=\"10.1186\/s13073-020-00747-0\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXhtVGmsLvI\" aria-label=\"CAS reference 5\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=32471482\" aria-label=\"PubMed reference 5\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7260799\" aria-label=\"PubMed Central reference 5\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 5\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Strain-resolved%20microbiome%20sequencing%20reveals%20mobile%20elements%20that%20drive%20bacterial%20competition%20on%20a%20clinical%20timescale&amp;journal=Genome%20Med.&amp;doi=10.1186%2Fs13073-020-00747-0&amp;volume=12&amp;publication_year=2020&amp;author=Zlitni%2CS\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR6\">Liu, Z. &amp; Good, B. H. Dynamics of bacterial recombination in the human gut microbiome. PLoS Biol. 22, e3002472 (2024).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1371\/journal.pbio.3002472\" data-track-item_id=\"10.1371\/journal.pbio.3002472\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1371%2Fjournal.pbio.3002472\" aria-label=\"Article reference 6\" data-doi=\"10.1371\/journal.pbio.3002472\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2cXjslWmsL8%3D\" aria-label=\"CAS reference 6\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=38329938\" aria-label=\"PubMed reference 6\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC10852326\" aria-label=\"PubMed Central reference 6\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 6\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Dynamics%20of%20bacterial%20recombination%20in%20the%20human%20gut%20microbiome&amp;journal=PLoS%20Biol.&amp;doi=10.1371%2Fjournal.pbio.3002472&amp;volume=22&amp;publication_year=2024&amp;author=Liu%2CZ&amp;author=Good%2CBH\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR7\">Smillie, C. S. et al. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480, 241\u2013244 (2011).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/nature10571\" data-track-item_id=\"10.1038\/nature10571\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fnature10571\" aria-label=\"Article reference 7\" data-doi=\"10.1038\/nature10571\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2011Natur.480..241S\" aria-label=\"ADS reference 7\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3MXhtlyisr7F\" aria-label=\"CAS reference 7\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=22037308\" aria-label=\"PubMed reference 7\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 7\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Ecology%20drives%20a%20global%20network%20of%20gene%20exchange%20connecting%20the%20human%20microbiome&amp;journal=Nature&amp;doi=10.1038%2Fnature10571&amp;volume=480&amp;pages=241-244&amp;publication_year=2011&amp;author=Smillie%2CCS\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR8\">Groussin, M. et al. Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell 184, 2053\u20132067 (2021).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.cell.2021.02.052\" data-track-item_id=\"10.1016\/j.cell.2021.02.052\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.cell.2021.02.052\" aria-label=\"Article reference 8\" data-doi=\"10.1016\/j.cell.2021.02.052\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3MXotVWhur4%3D\" aria-label=\"CAS reference 8\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=33794144\" aria-label=\"PubMed reference 8\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 8\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Elevated%20rates%20of%20horizontal%20gene%20transfer%20in%20the%20industrialized%20human%20microbiome&amp;journal=Cell&amp;doi=10.1016%2Fj.cell.2021.02.052&amp;volume=184&amp;pages=2053-2067&amp;publication_year=2021&amp;author=Groussin%2CM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR9\">McInnes, R. S., McCallum, G. E., Lamberte, L. E. &amp; van Schaik, W. Horizontal transfer of antibiotic resistance genes in the human gut microbiome. Curr. Opin. Microbiol. 53, 35\u201343 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.mib.2020.02.002\" data-track-item_id=\"10.1016\/j.mib.2020.02.002\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.mib.2020.02.002\" aria-label=\"Article reference 9\" data-doi=\"10.1016\/j.mib.2020.02.002\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXjvFWiurY%3D\" aria-label=\"CAS reference 9\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=32143027\" aria-label=\"PubMed reference 9\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 9\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Horizontal%20transfer%20of%20antibiotic%20resistance%20genes%20in%20the%20human%20gut%20microbiome&amp;journal=Curr.%20Opin.%20Microbiol.&amp;doi=10.1016%2Fj.mib.2020.02.002&amp;volume=53&amp;pages=35-43&amp;publication_year=2020&amp;author=McInnes%2CRS&amp;author=McCallum%2CGE&amp;author=Lamberte%2CLE&amp;author=Schaik%2CW\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR10\">Shapiro, B. J. et al. Population genomics of early events in the ecological differentiation of bacteria. Science 336, 48\u201351 (2012).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1126\/science.1218198\" data-track-item_id=\"10.1126\/science.1218198\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1126%2Fscience.1218198\" aria-label=\"Article reference 10\" data-doi=\"10.1126\/science.1218198\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2012Sci...336...48S\" aria-label=\"ADS reference 10\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC38XkvV2rs7w%3D\" aria-label=\"CAS reference 10\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=22491847\" aria-label=\"PubMed reference 10\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3337212\" aria-label=\"PubMed Central reference 10\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 10\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Population%20genomics%20of%20early%20events%20in%20the%20ecological%20differentiation%20of%20bacteria&amp;journal=Science&amp;doi=10.1126%2Fscience.1218198&amp;volume=336&amp;pages=48-51&amp;publication_year=2012&amp;author=Shapiro%2CBJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR11\">Shapiro, B. J. &amp; Polz, M. F. Ordering microbial diversity into ecologically and genetically cohesive units. Trends Microbiol. 22, 235\u2013247 (2014).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.tim.2014.02.006\" data-track-item_id=\"10.1016\/j.tim.2014.02.006\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.tim.2014.02.006\" aria-label=\"Article reference 11\" data-doi=\"10.1016\/j.tim.2014.02.006\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2cXkt1Smt7k%3D\" aria-label=\"CAS reference 11\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=24630527\" aria-label=\"PubMed reference 11\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4103024\" aria-label=\"PubMed Central reference 11\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 11\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Ordering%20microbial%20diversity%20into%20ecologically%20and%20genetically%20cohesive%20units&amp;journal=Trends%20Microbiol.&amp;doi=10.1016%2Fj.tim.2014.02.006&amp;volume=22&amp;pages=235-247&amp;publication_year=2014&amp;author=Shapiro%2CBJ&amp;author=Polz%2CMF\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR12\">Hudson, R. R., Bailey, K., Skarecky, D., Kwiatowski, J. &amp; Ayala, F. J. Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics 136, 1329\u20131340 (1994).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/genetics\/136.4.1329\" data-track-item_id=\"10.1093\/genetics\/136.4.1329\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fgenetics%2F136.4.1329\" aria-label=\"Article reference 12\" data-doi=\"10.1093\/genetics\/136.4.1329\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DyaK2cXmslOjtLc%3D\" aria-label=\"CAS reference 12\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=8013910\" aria-label=\"PubMed reference 12\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC1205914\" aria-label=\"PubMed Central reference 12\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 12\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Evidence%20for%20positive%20selection%20in%20the%20superoxide%20dismutase%20%28Sod%29%20region%20of%20Drosophila%20melanogaster&amp;journal=Genetics&amp;doi=10.1093%2Fgenetics%2F136.4.1329&amp;volume=136&amp;pages=1329-1340&amp;publication_year=1994&amp;author=Hudson%2CRR&amp;author=Bailey%2CK&amp;author=Skarecky%2CD&amp;author=Kwiatowski%2CJ&amp;author=Ayala%2CFJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR13\">Vitti, J. J., Grossman, S. R. &amp; Sabeti, P. C. Detecting natural selection in genomic data. Annu. Rev. Genet. 47, 97\u2013120 (2013).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1146\/annurev-genet-111212-133526\" data-track-item_id=\"10.1146\/annurev-genet-111212-133526\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1146%2Fannurev-genet-111212-133526\" aria-label=\"Article reference 13\" data-doi=\"10.1146\/annurev-genet-111212-133526\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2cXhsFOjtA%3D%3D\" aria-label=\"CAS reference 13\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=24274750\" aria-label=\"PubMed reference 13\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 13\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Detecting%20natural%20selection%20in%20genomic%20data&amp;journal=Annu.%20Rev.%20Genet.&amp;doi=10.1146%2Fannurev-genet-111212-133526&amp;volume=47&amp;pages=97-120&amp;publication_year=2013&amp;author=Vitti%2CJJ&amp;author=Grossman%2CSR&amp;author=Sabeti%2CPC\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR14\">Sabeti, P. C. et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832\u2013837 (2002).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/nature01140\" data-track-item_id=\"10.1038\/nature01140\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fnature01140\" aria-label=\"Article reference 14\" data-doi=\"10.1038\/nature01140\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2002Natur.419..832S\" aria-label=\"ADS reference 14\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD38XovF2itbc%3D\" aria-label=\"CAS reference 14\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=12397357\" aria-label=\"PubMed reference 14\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 14\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Detecting%20recent%20positive%20selection%20in%20the%20human%20genome%20from%20haplotype%20structure&amp;journal=Nature&amp;doi=10.1038%2Fnature01140&amp;volume=419&amp;pages=832-837&amp;publication_year=2002&amp;author=Sabeti%2CPC\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR15\">Voight, B. F., Kudaravalli, S., Wen, X. &amp; Pritchard, J. K. A map of recent positive selection in the human genome. PLoS Biol. 4, e72 (2006).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1371\/journal.pbio.0040072\" data-track-item_id=\"10.1371\/journal.pbio.0040072\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1371%2Fjournal.pbio.0040072\" aria-label=\"Article reference 15\" data-doi=\"10.1371\/journal.pbio.0040072\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=16494531\" aria-label=\"PubMed reference 15\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC1382018\" aria-label=\"PubMed Central reference 15\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 15\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20map%20of%20recent%20positive%20selection%20in%20the%20human%20genome&amp;journal=PLoS%20Biol.&amp;doi=10.1371%2Fjournal.pbio.0040072&amp;volume=4&amp;publication_year=2006&amp;author=Voight%2CBF&amp;author=Kudaravalli%2CS&amp;author=Wen%2CX&amp;author=Pritchard%2CJK\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR16\">Garud, N. R., Messer, P. W., Buzbas, E. O. &amp; Petrov, D. A. Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps. PLoS Genet. 11, e1005004 (2015).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1371\/journal.pgen.1005004\" data-track-item_id=\"10.1371\/journal.pgen.1005004\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1371%2Fjournal.pgen.1005004\" aria-label=\"Article reference 16\" data-doi=\"10.1371\/journal.pgen.1005004\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=25706129\" aria-label=\"PubMed reference 16\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4338236\" aria-label=\"PubMed Central reference 16\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 16\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Recent%20selective%20sweeps%20in%20North%20American%20Drosophila%20melanogaster%20show%20signatures%20of%20soft%20sweeps&amp;journal=PLoS%20Genet.&amp;doi=10.1371%2Fjournal.pgen.1005004&amp;volume=11&amp;publication_year=2015&amp;author=Garud%2CNR&amp;author=Messer%2CPW&amp;author=Buzbas%2CEO&amp;author=Petrov%2CDA\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR17\">Ferrer-Admetlla, A., Liang, M., Korneliussen, T. &amp; Nielsen, R. On detecting incomplete soft or hard selective sweeps using haplotype structure. Mol. Biol. Evol. 31, 1275\u20131291 (2014).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/molbev\/msu077\" data-track-item_id=\"10.1093\/molbev\/msu077\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fmolbev%2Fmsu077\" aria-label=\"Article reference 17\" data-doi=\"10.1093\/molbev\/msu077\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2cXmvFCiur8%3D\" aria-label=\"CAS reference 17\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=24554778\" aria-label=\"PubMed reference 17\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3995338\" aria-label=\"PubMed Central reference 17\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 17\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=On%20detecting%20incomplete%20soft%20or%20hard%20selective%20sweeps%20using%20haplotype%20structure&amp;journal=Mol.%20Biol.%20Evol.&amp;doi=10.1093%2Fmolbev%2Fmsu077&amp;volume=31&amp;pages=1275-1291&amp;publication_year=2014&amp;author=Ferrer-Admetlla%2CA&amp;author=Liang%2CM&amp;author=Korneliussen%2CT&amp;author=Nielsen%2CR\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR18\">Shapiro, B. J. Signatures of natural selection and ecological differentiation in microbial genomes. Adv. Exp. Med. Biol. 781, 339\u2013359 (2014).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener nofollow\" data-track-label=\"10.1007\/978-94-007-7347-9_17\" data-track-item_id=\"10.1007\/978-94-007-7347-9_17\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1007\/978-94-007-7347-9_17\" aria-label=\"Article reference 18\" data-doi=\"10.1007\/978-94-007-7347-9_17\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2MXlvFGltbY%3D\" aria-label=\"CAS reference 18\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=24277308\" aria-label=\"PubMed reference 18\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 18\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Signatures%20of%20natural%20selection%20and%20ecological%20differentiation%20in%20microbial%20genomes.&amp;journal=Adv.%20Exp.%20Med.%20Biol.&amp;doi=10.1007%2F978-94-007-7347-9_17&amp;volume=781&amp;pages=339-359&amp;publication_year=2014&amp;author=Shapiro%2CBJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR19\">Good, B. H., Bhatt, A. S. &amp; McDonald, M. J. Unraveling the tempo and mode of horizontal gene transfer in bacteria. Trends Microbiol. 33, 853\u2013865 (2025).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.tim.2025.03.009\" data-track-item_id=\"10.1016\/j.tim.2025.03.009\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.tim.2025.03.009\" aria-label=\"Article reference 19\" data-doi=\"10.1016\/j.tim.2025.03.009\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2MXpsFOjtrY%3D\" aria-label=\"CAS reference 19\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=40274494\" aria-label=\"PubMed reference 19\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 19\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Unraveling%20the%20tempo%20and%20mode%20of%20horizontal%20gene%20transfer%20in%20bacteria&amp;journal=Trends%20Microbiol.&amp;doi=10.1016%2Fj.tim.2025.03.009&amp;volume=33&amp;pages=853-865&amp;publication_year=2025&amp;author=Good%2CBH&amp;author=Bhatt%2CAS&amp;author=McDonald%2CMJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR20\">Pritchard, J. K. &amp; Przeworski, M. Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69, 1\u201314 (2001).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1086\/321275\" data-track-item_id=\"10.1086\/321275\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1086%2F321275\" aria-label=\"Article reference 20\" data-doi=\"10.1086\/321275\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD3MXls1emtro%3D\" aria-label=\"CAS reference 20\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=11410837\" aria-label=\"PubMed reference 20\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC1226024\" aria-label=\"PubMed Central reference 20\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 20\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Linkage%20disequilibrium%20in%20humans%3A%20models%20and%20data&amp;journal=Am.%20J.%20Hum.%20Genet.&amp;doi=10.1086%2F321275&amp;volume=69&amp;pages=1-14&amp;publication_year=2001&amp;author=Pritchard%2CJK&amp;author=Przeworski%2CM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR21\">Mah, J. C., Lohmueller, K. E. &amp; Garud, N. R. Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history. Mol. Biol. Evol. 42, msaf010 (2025).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/molbev\/msaf010\" data-track-item_id=\"10.1093\/molbev\/msaf010\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fmolbev%2Fmsaf010\" aria-label=\"Article reference 21\" data-doi=\"10.1093\/molbev\/msaf010\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2MXhtVOhsL7L\" aria-label=\"CAS reference 21\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=39838923\" aria-label=\"PubMed reference 21\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC11824422\" aria-label=\"PubMed Central reference 21\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 21\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Inference%20of%20the%20demographic%20histories%20and%20selective%20effects%20of%20human%20gut%20commensal%20microbiota%20over%20the%20course%20of%20human%20history&amp;journal=Mol.%20Biol.%20Evol.&amp;doi=10.1093%2Fmolbev%2Fmsaf010&amp;volume=42&amp;publication_year=2025&amp;author=Mah%2CJC&amp;author=Lohmueller%2CKE&amp;author=Garud%2CNR\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR22\">Eyre-Walker, A. &amp; Keightley, P. D. The distribution of fitness effects of new mutations. Nat. Rev. Genet. 8, 610\u2013618 (2007).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/nrg2146\" data-track-item_id=\"10.1038\/nrg2146\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fnrg2146\" aria-label=\"Article reference 22\" data-doi=\"10.1038\/nrg2146\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD2sXnvVekt7s%3D\" aria-label=\"CAS reference 22\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=17637733\" aria-label=\"PubMed reference 22\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 22\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20distribution%20of%20fitness%20effects%20of%20new%20mutations&amp;journal=Nat.%20Rev.%20Genet.&amp;doi=10.1038%2Fnrg2146&amp;volume=8&amp;pages=610-618&amp;publication_year=2007&amp;author=Eyre-Walker%2CA&amp;author=Keightley%2CPD\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR23\">Lawrie, D. S. &amp; Petrov, D. A. Comparative population genomics: power and principles for the inference of functionality. Trends Genet. 30, 133\u2013139 (2014).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.tig.2014.02.002\" data-track-item_id=\"10.1016\/j.tig.2014.02.002\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.tig.2014.02.002\" aria-label=\"Article reference 23\" data-doi=\"10.1016\/j.tig.2014.02.002\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2cXks1Ols7Y%3D\" aria-label=\"CAS reference 23\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=24656563\" aria-label=\"PubMed reference 23\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4073783\" aria-label=\"PubMed Central reference 23\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 23\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Comparative%20population%20genomics%3A%20power%20and%20principles%20for%20the%20inference%20of%20functionality&amp;journal=Trends%20Genet.&amp;doi=10.1016%2Fj.tig.2014.02.002&amp;volume=30&amp;pages=133-139&amp;publication_year=2014&amp;author=Lawrie%2CDS&amp;author=Petrov%2CDA\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR24\">Cvijovi\u0107, I., Good, B. H. &amp; Desai, M. M. The effect of strong purifying selection on genetic diversity. Genetics 209, 1235\u20131278 (2018).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1534\/genetics.118.301058\" data-track-item_id=\"10.1534\/genetics.118.301058\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1534%2Fgenetics.118.301058\" aria-label=\"Article reference 24\" data-doi=\"10.1534\/genetics.118.301058\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=29844134\" aria-label=\"PubMed reference 24\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6063222\" aria-label=\"PubMed Central reference 24\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 24\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20effect%20of%20strong%20purifying%20selection%20on%20genetic%20diversity&amp;journal=Genetics&amp;doi=10.1534%2Fgenetics.118.301058&amp;volume=209&amp;pages=1235-1278&amp;publication_year=2018&amp;author=Cvijovi%C4%87%2CI&amp;author=Good%2CBH&amp;author=Desai%2CMM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR25\">Hartfield, M. &amp; Otto, S. P. Recombination and hitchhiking of deleterious alleles. Evolution 65, 2421\u20132434 (2011).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1111\/j.1558-5646.2011.01311.x\" data-track-item_id=\"10.1111\/j.1558-5646.2011.01311.x\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1111%2Fj.1558-5646.2011.01311.x\" aria-label=\"Article reference 25\" data-doi=\"10.1111\/j.1558-5646.2011.01311.x\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=21884046\" aria-label=\"PubMed reference 25\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 25\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Recombination%20and%20hitchhiking%20of%20deleterious%20alleles&amp;journal=Evolution&amp;doi=10.1111%2Fj.1558-5646.2011.01311.x&amp;volume=65&amp;pages=2421-2434&amp;publication_year=2011&amp;author=Hartfield%2CM&amp;author=Otto%2CSP\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR26\">Haller, B. C. &amp; Messer, P. W. SLiM 4: Multispecies eco-evolutionary modeling. Am. Nat. 201, E127\u2013E139 (2023).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1086\/723601\" data-track-item_id=\"10.1086\/723601\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1086%2F723601\" aria-label=\"Article reference 26\" data-doi=\"10.1086\/723601\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=37130229\" aria-label=\"PubMed reference 26\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC10793872\" aria-label=\"PubMed Central reference 26\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 26\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=SLiM%204%3A%20Multispecies%20eco-evolutionary%20modeling&amp;journal=Am.%20Nat.&amp;doi=10.1086%2F723601&amp;volume=201&amp;pages=E127-E139&amp;publication_year=2023&amp;author=Haller%2CBC&amp;author=Messer%2CPW\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR27\">Lloyd-Price, J. et al. Strains, functions and dynamics in the expanded human microbiome project. Nature 550, 61\u201366 (2017).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/nature23889\" data-track-item_id=\"10.1038\/nature23889\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fnature23889\" aria-label=\"Article reference 27\" data-doi=\"10.1038\/nature23889\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2017Natur.550...61L\" aria-label=\"ADS reference 27\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2sXhsFehtrzE\" aria-label=\"CAS reference 27\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=28953883\" aria-label=\"PubMed reference 27\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5831082\" aria-label=\"PubMed Central reference 27\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 27\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Strains%2C%20functions%20and%20dynamics%20in%20the%20expanded%20human%20microbiome%20project&amp;journal=Nature&amp;doi=10.1038%2Fnature23889&amp;volume=550&amp;pages=61-66&amp;publication_year=2017&amp;author=Lloyd-Price%2CJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR28\">Xie, H. et al. Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome. Cell Systems 3, 572\u2013584 (2016).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.cels.2016.10.004\" data-track-item_id=\"10.1016\/j.cels.2016.10.004\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.cels.2016.10.004\" aria-label=\"Article reference 28\" data-doi=\"10.1016\/j.cels.2016.10.004\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2sXhtFalsLw%3D\" aria-label=\"CAS reference 28\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=27818083\" aria-label=\"PubMed reference 28\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6309625\" aria-label=\"PubMed Central reference 28\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 28\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Shotgun%20metagenomics%20of%20250%20adult%20twins%20reveals%20genetic%20and%20environmental%20impacts%20on%20the%20gut%20microbiome&amp;journal=Cell%20Systems&amp;doi=10.1016%2Fj.cels.2016.10.004&amp;volume=3&amp;pages=572-584&amp;publication_year=2016&amp;author=Xie%2CH\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR29\">Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55\u201360 (2012).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/nature11450\" data-track-item_id=\"10.1038\/nature11450\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fnature11450\" aria-label=\"Article reference 29\" data-doi=\"10.1038\/nature11450\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2012Natur.490...55Q\" aria-label=\"ADS reference 29\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC38XhsVaqt7fJ\" aria-label=\"CAS reference 29\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=23023125\" aria-label=\"PubMed reference 29\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 29\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20metagenome-wide%20association%20study%20of%20gut%20microbiota%20in%20type%202%20diabetes&amp;journal=Nature&amp;doi=10.1038%2Fnature11450&amp;volume=490&amp;pages=55-60&amp;publication_year=2012&amp;author=Qin%2CJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR30\">Korpela, K. et al. Selective maternal seeding and environment shape the human gut microbiome. Genome Res. 28, 561\u2013568 (2018).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1101\/gr.233940.117\" data-track-item_id=\"10.1101\/gr.233940.117\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1101%2Fgr.233940.117\" aria-label=\"Article reference 30\" data-doi=\"10.1101\/gr.233940.117\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1cXns1Cmt7Y%3D\" aria-label=\"CAS reference 30\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=29496731\" aria-label=\"PubMed reference 30\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5880245\" aria-label=\"PubMed Central reference 30\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 30\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Selective%20maternal%20seeding%20and%20environment%20shape%20the%20human%20gut%20microbiome&amp;journal=Genome%20Res.&amp;doi=10.1101%2Fgr.233940.117&amp;volume=28&amp;pages=561-568&amp;publication_year=2018&amp;author=Korpela%2CK\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR31\">Nayfach, S., Rodriguez-Mueller, B., Garud, N. &amp; Pollard, K. S. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res. 26, 1612\u20131625 (2016).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1101\/gr.201863.115\" data-track-item_id=\"10.1101\/gr.201863.115\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1101%2Fgr.201863.115\" aria-label=\"Article reference 31\" data-doi=\"10.1101\/gr.201863.115\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2sXhs1Ogsb4%3D\" aria-label=\"CAS reference 31\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=27803195\" aria-label=\"PubMed reference 31\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5088602\" aria-label=\"PubMed Central reference 31\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 31\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=An%20integrated%20metagenomics%20pipeline%20for%20strain%20profiling%20reveals%20novel%20patterns%20of%20bacterial%20transmission%20and%20biogeography&amp;journal=Genome%20Res.&amp;doi=10.1101%2Fgr.201863.115&amp;volume=26&amp;pages=1612-1625&amp;publication_year=2016&amp;author=Nayfach%2CS&amp;author=Rodriguez-Mueller%2CB&amp;author=Garud%2CN&amp;author=Pollard%2CKS\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR32\">Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat. Biotechnol. 39, 105\u2013114 (2021).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41587-020-0603-3\" data-track-item_id=\"10.1038\/s41587-020-0603-3\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41587-020-0603-3\" aria-label=\"Article reference 32\" data-doi=\"10.1038\/s41587-020-0603-3\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXhsVWgtL%2FN\" aria-label=\"CAS reference 32\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=32690973\" aria-label=\"PubMed reference 32\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 32\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20unified%20catalog%20of%20204%2C938%20reference%20genomes%20from%20the%20human%20gut%20microbiome&amp;journal=Nat.%20Biotechnol.&amp;doi=10.1038%2Fs41587-020-0603-3&amp;volume=39&amp;pages=105-114&amp;publication_year=2021&amp;author=Almeida%2CA\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR33\">Shen, E. et al. Subtyping analysis reveals new variants and accelerated evolution of Clostridioides difficile toxin b. Commun. Biol. 3, 347 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s42003-020-1078-y\" data-track-item_id=\"10.1038\/s42003-020-1078-y\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs42003-020-1078-y\" aria-label=\"Article reference 33\" data-doi=\"10.1038\/s42003-020-1078-y\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3MXhtV2iu73J\" aria-label=\"CAS reference 33\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=32620855\" aria-label=\"PubMed reference 33\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7335066\" aria-label=\"PubMed Central reference 33\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 33\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Subtyping%20analysis%20reveals%20new%20variants%20and%20accelerated%20evolution%20of%20Clostridioides%20difficile%20toxin%20b&amp;journal=Commun.%20Biol.&amp;doi=10.1038%2Fs42003-020-1078-y&amp;volume=3&amp;publication_year=2020&amp;author=Shen%2CE\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR34\">Mansfield, M. J. et al. Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B. PLoS Pathog. 16, e1009181 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1371\/journal.ppat.1009181\" data-track-item_id=\"10.1371\/journal.ppat.1009181\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1371%2Fjournal.ppat.1009181\" aria-label=\"Article reference 34\" data-doi=\"10.1371\/journal.ppat.1009181\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3MXjtlOhsbY%3D\" aria-label=\"CAS reference 34\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=33370413\" aria-label=\"PubMed reference 34\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7853461\" aria-label=\"PubMed Central reference 34\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 34\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Phylogenomics%20of%208%2C839%20Clostridioides%20difficile%20genomes%20reveals%20recombination-driven%20evolution%20and%20diversification%20of%20toxin%20A%20and%20B&amp;journal=PLoS%20Pathog.&amp;doi=10.1371%2Fjournal.ppat.1009181&amp;volume=16&amp;publication_year=2020&amp;author=Mansfield%2CMJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR35\">Dingle, K. E. et al. Recombinational switching of the Clostridium difficile S-layer and a novel glycosylation gene cluster revealed by large-scale whole-genome sequencing. J. Infect. Dis. 207, 675\u2013686 (2013).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/infdis\/jis734\" data-track-item_id=\"10.1093\/infdis\/jis734\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Finfdis%2Fjis734\" aria-label=\"Article reference 35\" data-doi=\"10.1093\/infdis\/jis734\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3sXhvV2itL4%3D\" aria-label=\"CAS reference 35\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=23204167\" aria-label=\"PubMed reference 35\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 35\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Recombinational%20switching%20of%20the%20Clostridium%20difficile%20S-layer%20and%20a%20novel%20glycosylation%20gene%20cluster%20revealed%20by%20large-scale%20whole-genome%20sequencing&amp;journal=J.%20Infect.%20Dis.&amp;doi=10.1093%2Finfdis%2Fjis734&amp;volume=207&amp;pages=675-686&amp;publication_year=2013&amp;author=Dingle%2CKE\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR36\">Steinberg, H. D. &amp; Snitkin, E. S. Homologous recombination in Clostridioides difficile mediates diversification of cell surface features and transport systems. mSphere 5, 10\u20131128 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1128\/mSphere.00799-20\" data-track-item_id=\"10.1128\/mSphere.00799-20\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1128%2FmSphere.00799-20\" aria-label=\"Article reference 36\" data-doi=\"10.1128\/mSphere.00799-20\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 36\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Homologous%20recombination%20in%20Clostridioides%20difficile%20mediates%20diversification%20of%20cell%20surface%20features%20and%20transport%20systems&amp;journal=mSphere&amp;doi=10.1128%2FmSphere.00799-20&amp;volume=5&amp;pages=10-1128&amp;publication_year=2020&amp;author=Steinberg%2CHD&amp;author=Snitkin%2CES\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR37\">Chen, D. W. &amp; Garud, N. R. Rapid evolution and strain turnover in the infant gut microbiome. Genome Res. 32, 1124\u20131136 (2022).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1101\/gr.276306.121\" data-track-item_id=\"10.1101\/gr.276306.121\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1101%2Fgr.276306.121\" aria-label=\"Article reference 37\" data-doi=\"10.1101\/gr.276306.121\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2cXit1CmsbzK\" aria-label=\"CAS reference 37\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=35545448\" aria-label=\"PubMed reference 37\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC9248880\" aria-label=\"PubMed Central reference 37\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 37\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Rapid%20evolution%20and%20strain%20turnover%20in%20the%20infant%20gut%20microbiome&amp;journal=Genome%20Res.&amp;doi=10.1101%2Fgr.276306.121&amp;volume=32&amp;pages=1124-1136&amp;publication_year=2022&amp;author=Chen%2CDW&amp;author=Garud%2CNR\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR38\">Tatusov, R. L., Galperin, M. Y., Natale, D. A. &amp; Koonin, E. V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33\u201336 (2000).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/nar\/28.1.33\" data-track-item_id=\"10.1093\/nar\/28.1.33\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fnar%2F28.1.33\" aria-label=\"Article reference 38\" data-doi=\"10.1093\/nar\/28.1.33\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD3cXhvVGqu7w%3D\" aria-label=\"CAS reference 38\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=10592175\" aria-label=\"PubMed reference 38\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC102395\" aria-label=\"PubMed Central reference 38\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 38\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20COG%20database%3A%20a%20tool%20for%20genome-scale%20analysis%20of%20protein%20functions%20and%20evolution&amp;journal=Nucleic%20Acids%20Res.&amp;doi=10.1093%2Fnar%2F28.1.33&amp;volume=28&amp;pages=33-36&amp;publication_year=2000&amp;author=Tatusov%2CRL&amp;author=Galperin%2CMY&amp;author=Natale%2CDA&amp;author=Koonin%2CEV\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR39\">Barrett, A. J. Enzyme nomenclature. Recommendations 1992: Supplement 2: Corrections and additions (1994). Eur. J. Biochem. 232, 1 (1995).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1111\/j.1432-1033.1995.tb20774.x\" data-track-item_id=\"10.1111\/j.1432-1033.1995.tb20774.x\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1111%2Fj.1432-1033.1995.tb20774.x\" aria-label=\"Article reference 39\" data-doi=\"10.1111\/j.1432-1033.1995.tb20774.x\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DyaK2MXnvVKks7s%3D\" aria-label=\"CAS reference 39\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=8690012\" aria-label=\"PubMed reference 39\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 39\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Enzyme%20nomenclature.%20Recommendations%201992%3A%20Supplement%202%3A%20Corrections%20and%20additions%20%281994%29&amp;journal=Eur.%20J.%20Biochem.&amp;doi=10.1111%2Fj.1432-1033.1995.tb20774.x&amp;volume=232&amp;publication_year=1995&amp;author=Barrett%2CAJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR40\">Grand, M., Riboulet-Bisson, E., Deutscher, J., Hartke, A. &amp; Sauvageot, N. Enterococcus faecalis maltodextrin gene regulation by combined action of maltose gene regulator MalR and pleiotropic regulator CcpA. Appl. Environ. Microbiol. 86, e01147\u201320 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1128\/AEM.01147-20\" data-track-item_id=\"10.1128\/AEM.01147-20\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1128%2FAEM.01147-20\" aria-label=\"Article reference 40\" data-doi=\"10.1128\/AEM.01147-20\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2020ApEnM..86E1147G\" aria-label=\"ADS reference 40\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXhvFKlu7bO\" aria-label=\"CAS reference 40\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=32680872\" aria-label=\"PubMed reference 40\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7480380\" aria-label=\"PubMed Central reference 40\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 40\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Enterococcus%20faecalis%20maltodextrin%20gene%20regulation%20by%20combined%20action%20of%20maltose%20gene%20regulator%20MalR%20and%20pleiotropic%20regulator%20CcpA&amp;journal=Appl.%20Environ.%20Microbiol.&amp;doi=10.1128%2FAEM.01147-20&amp;volume=86&amp;pages=e01147-20&amp;publication_year=2020&amp;author=Grand%2CM&amp;author=Riboulet-Bisson%2CE&amp;author=Deutscher%2CJ&amp;author=Hartke%2CA&amp;author=Sauvageot%2CN\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR41\">Arnold, A. R. &amp; Chassaing, B. Maltodextrin, modern stressor of the intestinal environment. Cell. Mol. Gastroenterol. Hepatol. 7, 475\u2013476 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.jcmgh.2018.09.014\" data-track-item_id=\"10.1016\/j.jcmgh.2018.09.014\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.jcmgh.2018.09.014\" aria-label=\"Article reference 41\" data-doi=\"10.1016\/j.jcmgh.2018.09.014\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=30827413\" aria-label=\"PubMed reference 41\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 41\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Maltodextrin%2C%20modern%20stressor%20of%20the%20intestinal%20environment&amp;journal=Cell.%20Mol.%20Gastroenterol.%20Hepatol.&amp;doi=10.1016%2Fj.jcmgh.2018.09.014&amp;volume=7&amp;pages=475-476&amp;publication_year=2019&amp;author=Arnold%2CAR&amp;author=Chassaing%2CB\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR42\">Ze, X., Duncan, S. H., Louis, P. &amp; Flint, H. J. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J. 6, 1535\u20131543 (2012).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/ismej.2012.4\" data-track-item_id=\"10.1038\/ismej.2012.4\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fismej.2012.4\" aria-label=\"Article reference 42\" data-doi=\"10.1038\/ismej.2012.4\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC38XhtVOjtL3L\" aria-label=\"CAS reference 42\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=22343308\" aria-label=\"PubMed reference 42\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3400402\" aria-label=\"PubMed Central reference 42\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 42\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Ruminococcus%20bromii%20is%20a%20keystone%20species%20for%20the%20degradation%20of%20resistant%20starch%20in%20the%20human%20colon&amp;journal=ISME%20J.&amp;doi=10.1038%2Fismej.2012.4&amp;volume=6&amp;pages=1535-1543&amp;publication_year=2012&amp;author=Ze%2CX&amp;author=Duncan%2CSH&amp;author=Louis%2CP&amp;author=Flint%2CHJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR43\">Shetty, S. A. et al. Inter-species metabolic interactions in an in-vitro minimal human gut microbiome of core bacteria. NPJ Biofilms Microbiomes 8, 21 (2022).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41522-022-00275-2\" data-track-item_id=\"10.1038\/s41522-022-00275-2\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41522-022-00275-2\" aria-label=\"Article reference 43\" data-doi=\"10.1038\/s41522-022-00275-2\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB38XhsFyjsLnN\" aria-label=\"CAS reference 43\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=35395818\" aria-label=\"PubMed reference 43\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC8993927\" aria-label=\"PubMed Central reference 43\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 43\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Inter-species%20metabolic%20interactions%20in%20an%20in-vitro%20minimal%20human%20gut%20microbiome%20of%20core%20bacteria&amp;journal=NPJ%20Biofilms%20Microbiomes&amp;doi=10.1038%2Fs41522-022-00275-2&amp;volume=8&amp;publication_year=2022&amp;author=Shetty%2CSA\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR44\">Sonnenburg, J. L. &amp; Sonnenburg, E. D. Vulnerability of the industrialized microbiota. Science 366, eaaw9255 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1126\/science.aaw9255\" data-track-item_id=\"10.1126\/science.aaw9255\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1126%2Fscience.aaw9255\" aria-label=\"Article reference 44\" data-doi=\"10.1126\/science.aaw9255\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXitVemtrjE\" aria-label=\"CAS reference 44\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=31649168\" aria-label=\"PubMed reference 44\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 44\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Vulnerability%20of%20the%20industrialized%20microbiota&amp;journal=Science&amp;doi=10.1126%2Fscience.aaw9255&amp;volume=366&amp;publication_year=2019&amp;author=Sonnenburg%2CJL&amp;author=Sonnenburg%2CED\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR45\">Brito, I. L. et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature 535, 435\u2013439 (2016).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/nature18927\" data-track-item_id=\"10.1038\/nature18927\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fnature18927\" aria-label=\"Article reference 45\" data-doi=\"10.1038\/nature18927\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2016Natur.535..435B\" aria-label=\"ADS reference 45\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC28Xht1yqsLnI\" aria-label=\"CAS reference 45\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=27409808\" aria-label=\"PubMed reference 45\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4983458\" aria-label=\"PubMed Central reference 45\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 45\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Mobile%20genes%20in%20the%20human%20microbiome%20are%20structured%20from%20global%20to%20individual%20scales&amp;journal=Nature&amp;doi=10.1038%2Fnature18927&amp;volume=535&amp;pages=435-439&amp;publication_year=2016&amp;author=Brito%2CIL\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR46\">Pasolli, E. et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell 176, 649\u2013662 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.cell.2019.01.001\" data-track-item_id=\"10.1016\/j.cell.2019.01.001\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.cell.2019.01.001\" aria-label=\"Article reference 46\" data-doi=\"10.1016\/j.cell.2019.01.001\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXhsVars7w%3D\" aria-label=\"CAS reference 46\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=30661755\" aria-label=\"PubMed reference 46\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6349461\" aria-label=\"PubMed Central reference 46\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 46\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Extensive%20unexplored%20human%20microbiome%20diversity%20revealed%20by%20over%20150%2C000%20genomes%20from%20metagenomes%20spanning%20age%2C%20geography%2C%20and%20lifestyle&amp;journal=Cell&amp;doi=10.1016%2Fj.cell.2019.01.001&amp;volume=176&amp;pages=649-662&amp;publication_year=2019&amp;author=Pasolli%2CE\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR47\">Obregon-Tito, A. J. et al. Subsistence strategies in traditional societies distinguish gut microbiomes. Nat. Commun. 6, 6505 (2015).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/ncomms7505\" data-track-item_id=\"10.1038\/ncomms7505\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fncomms7505\" aria-label=\"Article reference 47\" data-doi=\"10.1038\/ncomms7505\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2015NatCo...6.6505O\" aria-label=\"ADS reference 47\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2MXhtF2itb3M\" aria-label=\"CAS reference 47\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=25807110\" aria-label=\"PubMed reference 47\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 47\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Subsistence%20strategies%20in%20traditional%20societies%20distinguish%20gut%20microbiomes&amp;journal=Nat.%20Commun.&amp;doi=10.1038%2Fncomms7505&amp;volume=6&amp;publication_year=2015&amp;author=Obregon-Tito%2CAJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR48\">Pehrsson, E. C. et al. Interconnected microbiomes and resistomes in low-income human habitats. Nature 533, 212\u2013216 (2016).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/nature17672\" data-track-item_id=\"10.1038\/nature17672\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fnature17672\" aria-label=\"Article reference 48\" data-doi=\"10.1038\/nature17672\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2016Natur.533..212P\" aria-label=\"ADS reference 48\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC28XnvValsbo%3D\" aria-label=\"CAS reference 48\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=27172044\" aria-label=\"PubMed reference 48\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4869995\" aria-label=\"PubMed Central reference 48\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 48\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Interconnected%20microbiomes%20and%20resistomes%20in%20low-income%20human%20habitats&amp;journal=Nature&amp;doi=10.1038%2Fnature17672&amp;volume=533&amp;pages=212-216&amp;publication_year=2016&amp;author=Pehrsson%2CEC\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR49\">Liu, W. et al. Unique features of ethnic Mongolian gut microbiome revealed by metagenomic analysis. Sci. Rep. 6, 34826 (2016).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/srep34826\" data-track-item_id=\"10.1038\/srep34826\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fsrep34826\" aria-label=\"Article reference 49\" data-doi=\"10.1038\/srep34826\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2016NatSR...634826L\" aria-label=\"ADS reference 49\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC28Xhs1Cgt7vK\" aria-label=\"CAS reference 49\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=27708392\" aria-label=\"PubMed reference 49\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5052615\" aria-label=\"PubMed Central reference 49\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 49\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Unique%20features%20of%20ethnic%20Mongolian%20gut%20microbiome%20revealed%20by%20metagenomic%20analysis&amp;journal=Sci.%20Rep.&amp;doi=10.1038%2Fsrep34826&amp;volume=6&amp;publication_year=2016&amp;author=Liu%2CW\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR50\">Rosen, M. J., Davison, M., Bhaya, D. &amp; Fisher, D. S. Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche. Science 348, 1019\u20131023 (2015).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1126\/science.aaa4456\" data-track-item_id=\"10.1126\/science.aaa4456\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1126%2Fscience.aaa4456\" aria-label=\"Article reference 50\" data-doi=\"10.1126\/science.aaa4456\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2015Sci...348.1019R\" aria-label=\"ADS reference 50\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2MXovVKltLc%3D\" aria-label=\"CAS reference 50\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=26023139\" aria-label=\"PubMed reference 50\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 50\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Fine-scale%20diversity%20and%20extensive%20recombination%20in%20a%20quasisexual%20bacterial%20population%20occupying%20a%20broad%20niche&amp;journal=Science&amp;doi=10.1126%2Fscience.aaa4456&amp;volume=348&amp;pages=1019-1023&amp;publication_year=2015&amp;author=Rosen%2CMJ&amp;author=Davison%2CM&amp;author=Bhaya%2CD&amp;author=Fisher%2CDS\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR51\">Sakoparnig, T., Field, C. &amp; van Nimwegen, E. Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species. eLife 10, e65366 (2021).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.7554\/eLife.65366\" data-track-item_id=\"10.7554\/eLife.65366\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.7554%2FeLife.65366\" aria-label=\"Article reference 51\" data-doi=\"10.7554\/eLife.65366\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3MXhslahsrrI\" aria-label=\"CAS reference 51\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=33416498\" aria-label=\"PubMed reference 51\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7884076\" aria-label=\"PubMed Central reference 51\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 51\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Whole%20genome%20phylogenies%20reflect%20the%20distributions%20of%20recombination%20rates%20for%20many%20bacterial%20species&amp;journal=eLife&amp;doi=10.7554%2FeLife.65366&amp;volume=10&amp;publication_year=2021&amp;author=Sakoparnig%2CT&amp;author=Field%2CC&amp;author=Nimwegen%2CE\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR52\">Hehemann, J.-H. et al. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464, 908\u2013912 (2010).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/nature08937\" data-track-item_id=\"10.1038\/nature08937\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fnature08937\" aria-label=\"Article reference 52\" data-doi=\"10.1038\/nature08937\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2010Natur.464..908H\" aria-label=\"ADS reference 52\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3cXktlynsbw%3D\" aria-label=\"CAS reference 52\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=20376150\" aria-label=\"PubMed reference 52\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 52\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Transfer%20of%20carbohydrate-active%20enzymes%20from%20marine%20bacteria%20to%20Japanese%20gut%20microbiota&amp;journal=Nature&amp;doi=10.1038%2Fnature08937&amp;volume=464&amp;pages=908-912&amp;publication_year=2010&amp;author=Hehemann%2CJ-H\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR53\">Tourrette, E. et al. An ancient ecospecies of Helicobacter pylori. Nature 635, 178\u2013185 (2024).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41586-024-07991-z\" data-track-item_id=\"10.1038\/s41586-024-07991-z\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41586-024-07991-z\" aria-label=\"Article reference 53\" data-doi=\"10.1038\/s41586-024-07991-z\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2024Natur.635..178T\" aria-label=\"ADS reference 53\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2cXit1KltLrO\" aria-label=\"CAS reference 53\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=39415013\" aria-label=\"PubMed reference 53\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC11541087\" aria-label=\"PubMed Central reference 53\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 53\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=An%20ancient%20ecospecies%20of%20Helicobacter%20pylori.&amp;journal=Nature&amp;doi=10.1038%2Fs41586-024-07991-z&amp;volume=635&amp;pages=178-185&amp;publication_year=2024&amp;author=Tourrette%2CE\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR54\">Stolyarova, A. V. et al. Complex fitness landscape shapes variation in a hyperpolymorphic species. eLife 11, e76073 (2022).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.7554\/eLife.76073\" data-track-item_id=\"10.7554\/eLife.76073\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.7554%2FeLife.76073\" aria-label=\"Article reference 54\" data-doi=\"10.7554\/eLife.76073\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB38XitlCmsLvK\" aria-label=\"CAS reference 54\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=35532122\" aria-label=\"PubMed reference 54\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC9187340\" aria-label=\"PubMed Central reference 54\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 54\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Complex%20fitness%20landscape%20shapes%20variation%20in%20a%20hyperpolymorphic%20species&amp;journal=eLife&amp;doi=10.7554%2FeLife.76073&amp;volume=11&amp;publication_year=2022&amp;author=Stolyarova%2CAV\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR55\">Arnold, B. et al. Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen. Mol. Biol. Evol. 37, 417\u2013428 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/molbev\/msz225\" data-track-item_id=\"10.1093\/molbev\/msz225\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fmolbev%2Fmsz225\" aria-label=\"Article reference 55\" data-doi=\"10.1093\/molbev\/msz225\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXhslGlt7jJ\" aria-label=\"CAS reference 55\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=31589312\" aria-label=\"PubMed reference 55\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 55\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Fine-scale%20haplotype%20structure%20reveals%20strong%20signatures%20of%20positive%20selection%20in%20a%20recombining%20bacterial%20pathogen&amp;journal=Mol.%20Biol.%20Evol.&amp;doi=10.1093%2Fmolbev%2Fmsz225&amp;volume=37&amp;pages=417-428&amp;publication_year=2020&amp;author=Arnold%2CB\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR56\">Crits-Christoph, A., Olm, M. R., Diamond, S., Bouma-Gregson, K. &amp; Banfield, J. F. Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow. ISME J. 14, 1834\u20131846 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41396-020-0655-x\" data-track-item_id=\"10.1038\/s41396-020-0655-x\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41396-020-0655-x\" aria-label=\"Article reference 56\" data-doi=\"10.1038\/s41396-020-0655-x\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3cXot1ahur8%3D\" aria-label=\"CAS reference 56\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=32327732\" aria-label=\"PubMed reference 56\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7305173\" aria-label=\"PubMed Central reference 56\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 56\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Soil%20bacterial%20populations%20are%20shaped%20by%20recombination%20and%20gene-specific%20selection%20across%20a%20grassland%20meadow&amp;journal=ISME%20J.&amp;doi=10.1038%2Fs41396-020-0655-x&amp;volume=14&amp;pages=1834-1846&amp;publication_year=2020&amp;author=Crits-Christoph%2CA&amp;author=Olm%2CMR&amp;author=Diamond%2CS&amp;author=Bouma-Gregson%2CK&amp;author=Banfield%2CJF\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR57\">Callahan, B., Neher, R. A., Bachtrog, D., Andolfatto, P. &amp; Shraiman, B. I. Correlated evolution of nearby residues in drosophilid proteins. PLoS Genet. 7, e1001315 (2011).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1371\/journal.pgen.1001315\" data-track-item_id=\"10.1371\/journal.pgen.1001315\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1371%2Fjournal.pgen.1001315\" aria-label=\"Article reference 57\" data-doi=\"10.1371\/journal.pgen.1001315\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3MXjtVWjtLk%3D\" aria-label=\"CAS reference 57\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=21383965\" aria-label=\"PubMed reference 57\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3044683\" aria-label=\"PubMed Central reference 57\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 57\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Correlated%20evolution%20of%20nearby%20residues%20in%20drosophilid%20proteins&amp;journal=PLoS%20Genet.&amp;doi=10.1371%2Fjournal.pgen.1001315&amp;volume=7&amp;publication_year=2011&amp;author=Callahan%2CB&amp;author=Neher%2CRA&amp;author=Bachtrog%2CD&amp;author=Andolfatto%2CP&amp;author=Shraiman%2CBI\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR58\">Rocha, E. P. &amp; Feil, E. J. Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?. PLoS Genet. 6, e1001104 (2010).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1371\/journal.pgen.1001104\" data-track-item_id=\"10.1371\/journal.pgen.1001104\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1371%2Fjournal.pgen.1001104\" aria-label=\"Article reference 58\" data-doi=\"10.1371\/journal.pgen.1001104\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=20838590\" aria-label=\"PubMed reference 58\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2936526\" aria-label=\"PubMed Central reference 58\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 58\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Mutational%20patterns%20cannot%20explain%20genome%20composition%3A%20Are%20there%20any%20neutral%20sites%20in%20the%20genomes%20of%20bacteria%3F&amp;journal=PLoS%20Genet.&amp;doi=10.1371%2Fjournal.pgen.1001104&amp;volume=6&amp;publication_year=2010&amp;author=Rocha%2CEP&amp;author=Feil%2CEJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR59\">Schloissnig, S. et al. Genomic variation landscape of the human gut microbiome. Nature 493, 45\u201350 (2013).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/nature11711\" data-track-item_id=\"10.1038\/nature11711\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fnature11711\" aria-label=\"Article reference 59\" data-doi=\"10.1038\/nature11711\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2013Natur.493...45S\" aria-label=\"ADS reference 59\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=23222524\" aria-label=\"PubMed reference 59\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 59\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Genomic%20variation%20landscape%20of%20the%20human%20gut%20microbiome&amp;journal=Nature&amp;doi=10.1038%2Fnature11711&amp;volume=493&amp;pages=45-50&amp;publication_year=2013&amp;author=Schloissnig%2CS\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR60\">Assaf, Z. J., Petrov, D. A. &amp; Blundell, J. R. Obstruction of adaptation in diploids by recessive, strongly deleterious alleles. Proc. Natl Acad. Sci. USA 112, E2658\u2013E2666 (2015).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1073\/pnas.1424949112\" data-track-item_id=\"10.1073\/pnas.1424949112\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1073%2Fpnas.1424949112\" aria-label=\"Article reference 60\" data-doi=\"10.1073\/pnas.1424949112\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2015PNAS..112E2658A\" aria-label=\"ADS reference 60\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC2MXns1Olu7g%3D\" aria-label=\"CAS reference 60\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=25941393\" aria-label=\"PubMed reference 60\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4443376\" aria-label=\"PubMed Central reference 60\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 60\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Obstruction%20of%20adaptation%20in%20diploids%20by%20recessive%2C%20strongly%20deleterious%20alleles&amp;journal=Proc.%20Natl%20Acad.%20Sci.%20USA&amp;doi=10.1073%2Fpnas.1424949112&amp;volume=112&amp;pages=E2658-E2666&amp;publication_year=2015&amp;author=Assaf%2CZJ&amp;author=Petrov%2CDA&amp;author=Blundell%2CJR\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR61\">Arevalo, P., VanInsberghe, D., Elsherbini, J., Gore, J. &amp; Polz, M. F. A reverse ecology approach based on a biological definition of microbial populations. Cell 178, 820\u2013834 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.cell.2019.06.033\" data-track-item_id=\"10.1016\/j.cell.2019.06.033\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.cell.2019.06.033\" aria-label=\"Article reference 61\" data-doi=\"10.1016\/j.cell.2019.06.033\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXhsFKktrrE\" aria-label=\"CAS reference 61\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=31398339\" aria-label=\"PubMed reference 61\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 61\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20reverse%20ecology%20approach%20based%20on%20a%20biological%20definition%20of%20microbial%20populations&amp;journal=Cell&amp;doi=10.1016%2Fj.cell.2019.06.033&amp;volume=178&amp;pages=820-834&amp;publication_year=2019&amp;author=Arevalo%2CP&amp;author=VanInsberghe%2CD&amp;author=Elsherbini%2CJ&amp;author=Gore%2CJ&amp;author=Polz%2CMF\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR62\">Liu, B., Zheng, D., Zhou, S., Chen, L. &amp; Yang, J. VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res. 50, D912\u2013D917 (2022).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/nar\/gkab1107\" data-track-item_id=\"10.1093\/nar\/gkab1107\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fnar%2Fgkab1107\" aria-label=\"Article reference 62\" data-doi=\"10.1093\/nar\/gkab1107\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB38Xit1Gqsb4%3D\" aria-label=\"CAS reference 62\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=34850947\" aria-label=\"PubMed reference 62\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 62\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=VFDB%202022%3A%20a%20general%20classification%20scheme%20for%20bacterial%20virulence%20factors&amp;journal=Nucleic%20Acids%20Res.&amp;doi=10.1093%2Fnar%2Fgkab1107&amp;volume=50&amp;pages=D912-D917&amp;publication_year=2022&amp;author=Liu%2CB&amp;author=Zheng%2CD&amp;author=Zhou%2CS&amp;author=Chen%2CL&amp;author=Yang%2CJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR63\">Lack, J. B. et al. The Drosophila Genome Nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population. Genetics 199, 1229\u20131241 (2015).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR64\">Wolff, R. &amp; Garud, N. Gene-specific selective sweeps are pervasive across human gut microbiomes. Dryad <a href=\"http:\/\/datadryad.org\/dataset\/doi:10.5061\/dryad.9ghx3ffx4\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"http:\/\/datadryad.org\/dataset\/doi:10.5061\/dryad.9ghx3ffx4\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/datadryad.org\/dataset\/doi:10.5061\/dryad.9ghx3ffx4<\/a> (2025).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR65\">Wolff, R. &amp; Garud, N. Gene-specific selective sweeps are pervasive across human gut microbiomes. Zenodo <a href=\"https:\/\/doi.org\/10.5281\/zenodo.17253586\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.5281\/zenodo.17253586\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/doi.org\/10.5281\/zenodo.17253586<\/a> (2025).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR66\">Gangwer, K. A. et al. Molecular evolution of the Helicobacter pylori vacuolating toxin gene vacA. J. Bacteriol. 192, 6126\u20136135 (2010).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1128\/JB.01081-10\" data-track-item_id=\"10.1128\/JB.01081-10\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1128%2FJB.01081-10\" aria-label=\"Article reference 66\" data-doi=\"10.1128\/JB.01081-10\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3MXhs1Sitbo%3D\" aria-label=\"CAS reference 66\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=20870762\" aria-label=\"PubMed reference 66\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2981223\" aria-label=\"PubMed Central reference 66\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 66\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Molecular%20evolution%20of%20the%20Helicobacter%20pylori%20vacuolating%20toxin%20gene%20vacA&amp;journal=J.%20Bacteriol.&amp;doi=10.1128%2FJB.01081-10&amp;volume=192&amp;pages=6126-6135&amp;publication_year=2010&amp;author=Gangwer%2CKA\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n","protected":false},"excerpt":{"rendered":"Garud, N. R., Good, B. H., Hallatschek, O. &amp; Pollard, K. S. Evolutionary dynamics of bacteria in the&hellip;\n","protected":false},"author":2,"featured_media":190425,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[10],"tags":[134,1928,119138,1929,111,139,69,4594,147],"class_list":{"0":"post-190424","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-health","8":"tag-health","9":"tag-humanities-and-social-sciences","10":"tag-microbial-genetics","11":"tag-multidisciplinary","12":"tag-new-zealand","13":"tag-newzealand","14":"tag-nz","15":"tag-population-genetics","16":"tag-science"},"_links":{"self":[{"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/posts\/190424","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/comments?post=190424"}],"version-history":[{"count":0,"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/posts\/190424\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/media\/190425"}],"wp:attachment":[{"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/media?parent=190424"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/categories?post=190424"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.newsbeep.com\/nz\/wp-json\/wp\/v2\/tags?post=190424"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}