title: Bacteria from diverse habitats colonize and compete in the mouse gut.
abstract: To study how microbes establish themselves in a mammalian gut environment, we colonized germ-free mice with microbial communities from human, zebrafish, and termite guts, human skin and tongue, soil, and estuarine microbial mats. Bacteria from these foreign environments colonized and persisted in the mouse gut; their capacity to metabolize dietary and host carbohydrates and bile acids correlated with colonization success. Cohousing mice harboring these xenomicrobiota or a mouse cecal microbiota, along with germ-free "bystanders," revealed the success of particular bacterial taxa in invading guts with established communities and empty gut habitats. Unanticipated patterns of ecological succession were observed; for example, a soil-derived bacterium dominated even in the presence of bacteria from other gut communities (zebrafish and termite), and human-derived bacteria colonized germ-free bystander mice before mouse-derived organisms. This approach can be generalized to address a variety of mechanistic questions about succession, including succession in the context of microbiota-directed therapeutics.
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Henning
authors.initials: H
authors.lastname: Seedorf
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Nicholas W
authors.initials: NW
authors.lastname: Griffin
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Vanessa K
authors.initials: VK
authors.lastname: Ridaura
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Reyes
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Jiye
authors.initials: J
authors.lastname: Cheng
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Federico E
authors.initials: FE
authors.lastname: Rey
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Michelle I
authors.initials: MI
authors.lastname: Smith
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Gabriel M
authors.initials: GM
authors.lastname: Simon
authors.affiliation: Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, FL 33314, USA.
authors.forename: Rudolf H
authors.initials: RH
authors.lastname: Scheffrahn
authors.affiliation: Departments of Civil and Environmental Engineering and Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
authors.forename: Dagmar
authors.initials: D
authors.lastname: Woebken
authors.affiliation: Departments of Civil and Environmental Engineering and Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
authors.forename: Alfred M
authors.initials: AM
authors.lastname: Spormann
authors.affiliation: Biofrontiers Institute, University of Colorado, Boulder, Boulder, CO 80309, USA.
authors.forename: William
authors.initials: W
authors.lastname: Van Treuren
authors.affiliation: Biofrontiers Institute, University of Colorado, Boulder, Boulder, CO 80309, USA.
authors.forename: Luke K
authors.initials: LK
authors.lastname: Ursell
authors.affiliation: Biofrontiers Institute, University of Colorado, Boulder, Boulder, CO 80309, USA.
authors.forename: Megan
authors.initials: M
authors.lastname: Pirrung
authors.affiliation: Biofrontiers Institute, University of Colorado, Boulder, Boulder, CO 80309, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Robbins-Pianka
authors.affiliation: Centre National de la Recherche Scientifique, UMR 7257, 13288 Marseille, France.
authors.forename: Brandi L
authors.initials: BL
authors.lastname: Cantarel
authors.affiliation: Centre National de la Recherche Scientifique, UMR 7257, 13288 Marseille, France; Aix-Marseille Université, UMR 7257, 13288 Marseille, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Lombard
authors.affiliation: Centre National de la Recherche Scientifique, UMR 7257, 13288 Marseille, France; Aix-Marseille Université, UMR 7257, 13288 Marseille, France.
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.affiliation: Biofrontiers Institute, University of Colorado, Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA.
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA. Electronic address: jgordon@wustl.edu.
authors.forename: Jeffrey I
authors.initials: JI
authors.lastname: Gordon
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000254:growth & development* / Q000378:metabolism; D017753:Ecosystem; D063366:Estuaries; D041981:Gastrointestinal Tract / Q000382:microbiology*; D005856:Germ-Free Life; D006801:Humans; D020049:Isoptera / Q000382:microbiology; D051379:Mice / Q000382:microbiology*; D056265:Microbial Interactions; D012867:Skin / Q000382:microbiology; D012988:Soil Microbiology; D013559:Symbiosis; D014059:Tongue / Q000382:microbiology; D015027:Zebrafish / Q000382:microbiology