Open Access Highly Accessed Open Badges Research

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

Nicola Segata1, Susan Kinder Haake23, Peter Mannon4, Katherine P Lemon56, Levi Waldron1, Dirk Gevers7, Curtis Huttenhower1 and Jacques Izard58*

Author affiliations

1 Department of Biostatistics, 677 Huntington Avenue, Harvard School of Public Health, Boston, MA 02115, USA

2 Section of Periodontics, UCLA School of Dentistry, 10833 Le Conte Ave, Los Angeles, CA 90095, USA

3 Dental Research Institute, UCLA School of Dentistry, 10833 Le Conte Ave, Los Angeles, CA 90095, USA

4 Division of Gastroenterology and Hepatology, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35205, USA

5 Department of Molecular Genetics, 245 First Street, The Forsyth Institute, Cambridge, MA 02142, USA

6 Division of Infectious Diseases, Children's Hospital Boston, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA

7 Microbial Systems and Communities, Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA

8 Department of Oral Medicine, Infection and Immunity, 188 Longwood Ave, Harvard School of Dental Medicine, Boston, MA 02115, USA

For all author emails, please log on.

Citation and License

Genome Biology 2012, 13:R42  doi:10.1186/gb-2012-13-6-r42

Published: 14 June 2012



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.


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.


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.