Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

被引:750
作者
Segata, Nicola [2 ]
Haake, Susan Kinder [3 ,4 ]
Mannon, Peter [5 ]
Lemon, Katherine P. [1 ,6 ]
Waldron, Levi [2 ]
Gevers, Dirk [7 ]
Huttenhower, Curtis [2 ]
Izard, Jacques [1 ,8 ]
机构
[1] Forsyth Inst, Dept Mol Genet, Cambridge, MA 02142 USA
[2] Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA
[3] Univ Calif Los Angeles, Sect Periodont, Sch Dent, Los Angeles, CA 90095 USA
[4] Univ Calif Los Angeles, Sch Dent, Dent Res Inst, Los Angeles, CA 90095 USA
[5] Univ Alabama Birmingham, Div Gastroenterol & Hepatol, Birmingham, AL 35205 USA
[6] Harvard Univ, Sch Med, Div Infect Dis, Childrens Hosp Boston, Boston, MA 02115 USA
[7] Broad Inst MIT & Harvard, Cambridge Ctr 7, Microbial Syst & Communities Genome Sequencing &, Cambridge, MA 02142 USA
[8] Harvard Univ, Sch Dent Med, Dept Oral Med Infect & Immun, Boston, MA 02115 USA
来源
GENOME BIOLOGY | 2012年 / 13卷 / 06期
基金
美国国家科学基金会; 美国国家卫生研究院;
关键词
HUMAN GUT MICROBIOTA; GEN; NOV; INTESTINAL MICROBIOTA; MOLECULAR ANALYSIS; HYDROGEN-SULFIDE; ORAL-CAVITY; DIVERSITY; COMMUNITY; EVOLUTION; OBESITY;
D O I
10.1186/gb-2012-13-6-r42
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. The digestive tract includes diverse habitats and hosts the human body's greatest bacterial density. We describe the bacterial community composition of ten digestive tract sites from more than 200 normal adults enrolled in the Human Microbiome Project, and metagenomically determined metabolic potentials of four representative sites. Results: The microbiota of these diverse habitats formed four groups based on similar community compositions: buccal mucosa, keratinized gingiva, hard palate; saliva, tongue, tonsils, throat; sub-and supra-gingival plaques; and stool. Phyla initially identified from environmental samples were detected throughout this population, primarily TM7, SR1, and Synergistetes. Genera with pathogenic members were well-represented among this disease-free cohort. Tooth-associated communities were distinct, but not entirely dissimilar, from other oral surfaces. The Porphyromonadaceae, Veillonellaceae and Lachnospiraceae families were common to all sites, but the distributions of their genera varied significantly. Most metabolic processes were distributed widely throughout the digestive tract microbiota, with variations in metagenomic abundance between body habitats. These included shifts in sugar transporter types between the supragingival plaque, other oral surfaces, and stool; hydrogen and hydrogen sulfide production were also differentially distributed. Conclusions: The microbiomes of ten digestive tract sites separated into four types based on composition. A core set of metabolic pathways was present across these diverse digestive tract habitats. These data provide a critical baseline for future studies investigating local and systemic diseases affecting human health.
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页数:18
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