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One of the factors contributing to this change is colonization from the environment. The colonization of initially microbe-free hosts is particularly interesting, as their microbiome depends entirely on microbes of external origin. We present a mathematical model of this process with a particular emphasis on the effect of ecological drift and a finite host lifespan. Our results indicate the host lifespan becomes especially relevant for short-living organisms (e.g. <jats:italic>Caenorhabditis elegans<\/jats:italic>, <jats:italic>Drosophila melanogaster<\/jats:italic>, and <jats:italic>Danio rerio<\/jats:italic>). In this case, alternative microbiome states (often called enterotypes), the coexistence of microbe-free and colonized hosts, and a reduced probability of colonization can be observed in our model. These results unify multiple reported observations around colonization and suggest that no selective or deterministic drivers are necessary to explain them.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008392","type":"journal-article","created":{"date-parts":[[2020,11,2]],"date-time":"2020-11-02T18:48:41Z","timestamp":1604342921000},"page":"e1008392","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":16,"title":["Stochastic colonization of hosts with a finite lifespan can drive individual host microbes out of equilibrium"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0221-0936","authenticated-orcid":true,"given":"Rom\u00e1n","family":"Zapi\u00e9n-Campos","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2703-3665","authenticated-orcid":true,"given":"Michael","family":"Sieber","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0669-5267","authenticated-orcid":true,"given":"Arne","family":"Traulsen","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,11,2]]},"reference":[{"issue":"4","key":"pcbi.1008392.ref001","doi-asserted-by":"crossref","DOI":"10.1128\/MMBR.00002-17","article-title":"Stochastic community assembly: Does it matter in microbial ecology?","volume":"81","author":"J Zhou","year":"2017","journal-title":"Microbiology and Molecular Biology Reviews"},{"key":"pcbi.1008392.ref002","volume-title":"Monographs in Population Biology","author":"SP Hubbell","year":"2001"},{"issue":"4","key":"pcbi.1008392.ref003","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1111\/j.1462-2920.2005.00956.x","article-title":"Quantifying the roles of immigration and chance in shaping prokaryote community structure","volume":"8","author":"WT Sloan","year":"2006","journal-title":"Environmental Microbiology"},{"issue":"2","key":"pcbi.1008392.ref004","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1111\/j.1574-6941.2007.00379.x","article-title":"Neutral assembly of bacterial communities","volume":"62","author":"S Woodcock","year":"2007","journal-title":"FEMS Microbiology Ecology"},{"issue":"3","key":"pcbi.1008392.ref005","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/ismej.2015.142","article-title":"Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development","volume":"10","author":"AR Burns","year":"2016","journal-title":"The ISME Journal"},{"key":"pcbi.1008392.ref006","article-title":"Microbial community assembly in wild populations of the fruit fly Drosophila melanogaster","author":"KL Adair","year":"2018","journal-title":"The ISME Journal"},{"issue":"6","key":"pcbi.1008392.ref007","doi-asserted-by":"crossref","first-page":"e3000298","DOI":"10.1371\/journal.pbio.3000298","article-title":"Neutrality in the Metaorganism","volume":"17","author":"M Sieber","year":"2019","journal-title":"PLoS Biology"},{"issue":"3","key":"pcbi.1008392.ref008","doi-asserted-by":"crossref","first-page":"e2000633","DOI":"10.1371\/journal.pbio.2000633","article-title":"Stochastic assembly produces heterogeneous communities in the Caenorhabditis elegans intestine","volume":"15","author":"NM Vega","year":"2017","journal-title":"PLoS Biology"},{"issue":"7","key":"pcbi.1008392.ref009","doi-asserted-by":"crossref","first-page":"e1004365","DOI":"10.1371\/journal.pcbi.1004365","article-title":"Neutral models of microbiome evolution","volume":"11","author":"Q Zeng","year":"2015","journal-title":"PLoS Computational Biology"},{"issue":"41","key":"pcbi.1008392.ref010","doi-asserted-by":"crossref","first-page":"20591","DOI":"10.1073\/pnas.1909790116","article-title":"The role of multilevel selection in host microbiome evolution","volume":"116","author":"S Van Vliet","year":"2019","journal-title":"PNAS"},{"issue":"2","key":"pcbi.1008392.ref011","article-title":"Holobiont Evolution: Mathematical Model with Vertical Vs. 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