title: Cospeciation of gut microbiota with hominids.
abstract: The evolutionary origins of the bacterial lineages that populate the human gut are unknown. Here we show that multiple lineages of the predominant bacterial taxa in the gut arose via cospeciation with humans, chimpanzees, bonobos, and gorillas over the past 15 million years. Analyses of strain-level bacterial diversity within hominid gut microbiomes revealed that clades of Bacteroidaceae and Bifidobacteriaceae have been maintained exclusively within host lineages across hundreds of thousands of host generations. Divergence times of these cospeciating gut bacteria are congruent with those of hominids, indicating that nuclear, mitochondrial, and gut bacterial genomes diversified in concert during hominid evolution. This study identifies human gut bacteria descended from ancient symbionts that speciated simultaneously with humans and the African apes.
authors.affiliation: Department of Integrative Biology, 2506 Speedway A5000, University of Texas at Austin, Austin, TX 78712, USA. Miller Institute for Basic Research in Science, 2536 Channing Way, University of California, Berkeley, CA 94720, USA.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Moeller
authors.affiliation: Corpoicá C.I Tibaitata, Santa Fe de Bogotá, Bogotá, Colombia.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Caro-Quintero
authors.affiliation: Gombe Stream Research Center, Kigoma, Tanzania.
authors.forename: Deus
authors.initials: D
authors.lastname: Mjungu
authors.affiliation: Department of Anthropology, Northwestern University, 1810 Hinman Avenue, Evanston, IL 60208, USA. Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA.
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Georgiev
authors.affiliation: Department of Psychology and Biological Foundations of Behavior Program, LSP 261B, Franklin and Marshall College, Lancaster, PA 17603, USA.
authors.forename: Elizabeth V
authors.initials: EV
authors.lastname: Lonsdorf
authors.affiliation: Department of Anthropology, University of New Mexico, MSC01-1040, Albuquerque, NM 87131, USA.
authors.forename: Martin N
authors.initials: MN
authors.lastname: Muller
authors.affiliation: Department of Evolutionary Anthropology, 101 Biological Sciences Building, Duke University, Durham, NC 27708, USA.
authors.forename: Anne E
authors.initials: AE
authors.lastname: Pusey
authors.affiliation: Institut de Recherche pour le Développement, University of Montpellier, 34394 Montpellier, France.
authors.forename: Martine
authors.initials: M
authors.lastname: Peeters
authors.affiliation: Departments of Medicine and Microbiology, Perelman School of Medicine, 409 Johnson Pavilion, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Beatrice H
authors.initials: BH
authors.lastname: Hahn
authors.affiliation: Department of Integrative Biology, 2506 Speedway A5000, University of Texas at Austin, Austin, TX 78712, USA. howard.ochman@austin.utexas.edu.
authors.forename: Howard
authors.initials: H
authors.lastname: Ochman
mesh_terms: D039903:Actinobacteria / Q000145:classification* / Q000235:genetics / Q000502:physiology; D000818:Animals; D001438:Bacteroidaceae / Q000145:classification* / Q000235:genetics / Q000502:physiology; D005075:Biological Evolution; D002467:Cell Nucleus; D000069196:Gastrointestinal Microbiome / Q000235:genetics / Q000502:physiology*; D016680:Genome, Bacterial; D054629:Genome, Mitochondrial; D015186:Hominidae / Q000382:microbiology*; D006801:Humans; D010802:Phylogeny; D013045:Species Specificity; D013559:Symbiosis