Evolution of symbiotic bacteria in the distal human intestine

• Published in: PLoS biology 2007-07, Vol.5 (7), p.e156
• Main Authors: Xu, Jian, Mahowald, Michael A, Ley, Ruth E, Lozupone, Catherine A, Hamady, Micah, Martens, Eric C, Henrissat, Bernard, Coutinho, Pedro M, Minx, Patrick, Latreille, Philippe, Cordum, Holland, Van Brunt, Andrew, Kim, Kyung, Fulton, Robert S, Fulton, Lucinda A, Clifton, Sandra W, Wilson, Richard K, Knight, Robin D, Gordon, Jeffrey I
• Format: Article
• Language: English
• Subjects: Adaptation, Physiological; Bacteria; bacterial genomics; Bacteriology; Bacteriophages - genetics; Bacteroides - genetics; Bacteroides - physiology; Bacteroides - virology; BASIC BIOLOGICAL SCIENCES; Binomial distribution; Computational Biology; Conjugation, Genetic; DNA Transposable Elements; Ecology; Ecosystem; Eubacteria; Evolution, Molecular; Evolutionary Biology; Gastroenterology and Hepatology; Gene amplification; Gene Duplication; Gene Transfer, Horizontal; genetic loci; Genetic Variation; Genetics and Genomics; Genome, Bacterial; Genomes; Genomics; gut bacteria; Health aspects; Homo (Human); Human beings; human genomics; Humans; Intestines; Intestines - microbiology; Man; Microbial genetics; Microbiology; Molecular evolution; Molecular Sequence Data; phylogenetic analysis; Phylogeny; Physiological aspects; polysaccharides; Polysaccharides, Bacterial - biosynthesis; Polysaccharides, Bacterial - genetics; RNA, Bacterial - genetics; RNA, Ribosomal, 16S - genetics; sequence alignment; Species Specificity; Symbiosis - genetics
• ISSN: 1545-7885; 1544-9173; 1545-7885
• DOI: 10.1371/journal.pbio.0050156

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.