title: Unraveling the processes shaping mammalian gut microbiomes over evolutionary time.
abstract: Whether mammal-microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny and major dietary shifts have affected the distribution of different gut bacterial lineages and did so on vastly different bacterial phylogenetic resolutions. Diet mostly influences the acquisition of ancient and large microbial lineages. Conversely, correlation with host phylogeny is mostly seen among more recently diverged bacterial lineages, consistent with processes operating at similar timescales to host evolution. Considering microbiomes at appropriate phylogenetic scales allows us to model their evolution along the mammalian tree and to infer ancient diets from the predicted microbiomes of mammalian ancestors. Phylogenetic analyses support co-speciation as having a significant role in the evolution of mammalian gut microbiome compositions. Highly co-speciating bacterial genera are also associated with immune diseases in humans, laying a path for future studies that probe these co-speciating bacteria for signs of co-evolution.
authors.affiliation: Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Groussin
authors.affiliation: Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041, Grenoble Cedex 9, France.
authors.forename: Florent
authors.identifier: 0000-0003-0572-9901
authors.initials: F
authors.lastname: Mazel
authors.affiliation: Organismic and Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, Massachusetts 02138, USA.
authors.forename: Jon G
authors.initials: JG
authors.lastname: Sanders
authors.affiliation: Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.|The Broad Institute of MIT and Harvard, 415 Main Street Cambridge, Massachusetts 02142, USA.
authors.forename: Chris S
authors.initials: CS
authors.lastname: Smillie
authors.affiliation: Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041, Grenoble Cedex 9, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Lavergne
authors.affiliation: Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041, Grenoble Cedex 9, France.
authors.forename: Wilfried
authors.initials: W
authors.lastname: Thuiller
authors.affiliation: Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.|The Broad Institute of MIT and Harvard, 415 Main Street Cambridge, Massachusetts 02142, USA.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Alm
mesh_terms: D000818:Animals; D001419:Bacteria / Q000378:metabolism; D005075:Biological Evolution; D004032:Diet; D000069196:Gastrointestinal Microbiome; D060434:Herbivory / Q000502:physiology; D006801:Humans; D040582:Inheritance Patterns / Q000235:genetics; D008322:Mammals / Q000382:microbiology*; D010802:Phylogeny; D013045:Species Specificity; D013559:Symbiosis; D013997:Time Factors