title: Evolution of symbiotic bacteria in the distal human intestine.
abstract: The adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies. Little is known about the selective pressures that have shaped and are shaping this community's component species, which are dominated by members of the Bacteroidetes and Firmicutes divisions. To examine how the intestinal environment affects microbial genome evolution, we have sequenced the genomes of two members of the normal distal human gut microbiota, Bacteroides vulgatus and Bacteroides distasonis, and by comparison with the few other sequenced gut and non-gut Bacteroidetes, analyzed their niche and habitat adaptations. The results show that lateral gene transfer, mobile elements, and gene amplification have played important roles in affecting the ability of gut-dwelling Bacteroidetes to vary their cell surface, sense their environment, and harvest nutrient resources present in the distal intestine. Our findings show that these processes have been a driving force in the adaptation of Bacteroidetes to the distal gut environment, and emphasize the importance of considering the evolution of humans from an additional perspective, namely the evolution of our microbiomes.
authors.affiliation: Center for Genome Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
authors.forename: Michael A
authors.initials: MA
authors.lastname: Mahowald
authors.forename: Ruth E
authors.initials: RE
authors.lastname: Ley
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Lozupone
authors.forename: Micah
authors.initials: M
authors.lastname: Hamady
authors.forename: Eric C
authors.initials: EC
authors.lastname: Martens
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.forename: Pedro M
authors.initials: PM
authors.lastname: Coutinho
authors.forename: Patrick
authors.initials: P
authors.lastname: Minx
authors.forename: Philippe
authors.initials: P
authors.lastname: Latreille
authors.forename: Holland
authors.initials: H
authors.lastname: Cordum
authors.forename: Andrew
authors.initials: A
authors.lastname: Van Brunt
authors.forename: Kyung
authors.initials: K
authors.lastname: Kim
authors.forename: Robert S
authors.initials: RS
authors.lastname: Fulton
authors.forename: Lucinda A
authors.initials: LA
authors.lastname: Fulton
authors.forename: Sandra W
authors.initials: SW
authors.lastname: Clifton
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.forename: Robin D
authors.initials: RD
authors.lastname: Knight
authors.forename: Jeffrey I
authors.initials: JI
authors.lastname: Gordon
mesh_terms: D000222:Adaptation, Physiological; D001435:Bacteriophages / Q000235:genetics; D001439:Bacteroides / Q000235:genetics* / Q000502:physiology / Q000821:virology; D003227:Conjugation, Genetic; D004251:DNA Transposable Elements; D017753:Ecosystem; D019143:Evolution, Molecular; D020440:Gene Duplication; D022761:Gene Transfer, Horizontal; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D007422:Intestines / Q000382:microbiology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D011135:Polysaccharides, Bacterial / Q000096:biosynthesis / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013045:Species Specificity; D013559:Symbiosis / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D011135:Polysaccharides, Bacterial; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S