Abstract
BackgroundTo 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.ResultsThe 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.ConclusionsThe 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.
Highlights
To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease
Microbial community structure indicates four distinct community types within the ten digestive tract sites At all phylogenetic levels, from phylum to genus, we identified four groups of body habitats that maintain a distinct pattern of numerically dominant bacterial taxa as profiled using the 16S rRNA gene (Figure 1a), as classified by the Ribosome Database Project (RDP) [29]
Group 3, which consisted of both tooth plaque sites, had a further decrease in Firmicutes compared to Groups 1 and 2, with a marked increase in the relative abundance of Actinobacteria
Summary
To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. 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 HMP includes over 200 subjects and has collected microbiome samples from 15 to 18 body habitats per person [10]. This unique dataset permits novel studies of the human digestive tract within a large number of subjects, allows for comparisons of microbial communities between habitats, and enables the definition of distinct metabolic niches within and among individuals. The recruitment criteria included a set of objective, composite measurements performed by healthcare professionals [10], defining this reference population and enabling this investigation to focus on defining the integrated oral, oropharyngeal, and gut microbiomes in the absence of host disease
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