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

Abstract

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.

Figure 1

Groups detected in the sampled digestive tract microbiome sites based on similarities in microbial composition. (a) Taxonomic composition of the microbiota in the ten digestive tract body habitats investigated based on average relative abundance of 16S rRNA pyrosequencing reads assigned to phylum (upper chart) and genus (lower chart). Microbiota from the ten habitats are grouped based on the ratio of Firmicutes to Bacteroidetes as follows: Group 1 (G1), buccal mucosa (BM), keratinized gingiva (KG) and hard palate (HP); Group 2 (G2), throat (Th), palatine tonsils (PT), tongue dorsum (TD) and saliva (Sal); Group 3 (G3), supraginval (SupP) and subgingival plaques (SubP); and Group 4 (G4), stool (Stool). Labels indicate genera at average relative abundance ≥2% in at least one body site. The remaining genera were binned together in each phylum as 'other' along with the fraction of reads that could not be assigned at the genus level as 'unclassified' (uncl.). See Additional file 1 for detailed values. (b) Circular cladogram reporting taxa consistently differential among the body habitats in at least one group detected using LEfSe. Colors indicate the group in which each differential clade was most abundant. See Additional file 3 for the detailed list of taxa whose representation was statistically different among the groups. The representation is based on RDP phylogenetic hierarchy.

Figure 2

Noticeable relative abundance and variability of TM7, Synergistetes, and SR1 per body habitat. Representation of the relative abundances of the phyla TM7, Synergistetes (Synerg.), and SR1 among the subject population, expressed as percentage on a log scale (left). The high relative abundances of members of these phyla among the subjects, in particular for TM7, indicate a potential role in eubiosis. The body habitats and groups are labeled as in Figure 1.

Figure 3

Most microbes in the digestive tract communities vary widely in relative abundance among body habitats and individuals. Genera with the lowest (top) to highest (bottom) variability among samples spanning all ten body sites, with coefficients of variation reported numerically (right column) and relative abundance colored on a log scale. The scale bar shows the color-coding of the average relative abundance expressed as percentage, from low (black) to high (red). All genera present >0.001% in at least half of the samples are reported. Prevotella, Veillonella, and Streptococcus are least variable across both body sites and individuals.

Figure 4

Genera within the Porphyromonadaceae, Veillonellaceae and Lachnospiraceae families are differentially abundant across microbial communities between the upper and lower digestive tract. These three families were detected among all ten digestive body habitats, but genera within them showed varying patterns of niche specialization to sites along the digestive tract. All genera with at least 0.001% abundance in at least one body site are reported here. Clades showing a statistically significant difference (by LEfSe) specifically between oral and stool samples are indiocated with asterisks. Abundances are reported on a log scale as averages. The scale bar shows the color-coding of the average relative abundance expressed as percentage, from low (black) to high (red). The Porphyromonadaceae family is interesting in that its average abundances are higher in the gut than in the oral body habitats, but specific genera within the family diverge: Tannerella and Porphyromonas are predominantly present in the oral cavity, whereas Parabacteroides, Barnesiella, Odoribacter and Butyricimonas show higher relative abundances in the gut. BM, buccal mucosa; KG, keratinized gingiva; HP, hard palate; Th, throat; PT, palatine tonsils; TD, tongue dorsum; Sal, saliva; SupP, supraginval; SubP, subgingival plaques.

Figure 5

Niche specialization is widespread throughout the digestive tract even among adjacent body habitats. (a) Circular cladogram based on the RDP Taxonomy [29] reporting taxa significantly more abundant in supragingival (red) and subgingival plaque (green) and demonstrating the extensive specialization even at these highly related sites. At the class level, Actinobacteria, Bacilli, Gamma-proteobacteria, Beta-proteobacteria, and Flavobacteria are characteristic of the supragingival plaque, whereas Fusobacteria, Clostridia, Epsilon-proteobacteria, Spirochaetes, Bacteroidia, and unclassified Bacteroidetes are biomarkers for the subgingival plaque. (b) Circular cladogram comparing the digestive tract (red, GI) with non-mucosal body habitats (green, NON-GI: comprising samples from the anterior nares, and from the bilateral skin sites, antecubital fossae, and retroauricular creases). Only a few clades are detected as differentially present and abundant throughout the entire digestive tract, as the high degree of specialization and community variability at each body site prevents any individual community member from being representative of all ten body habitats. BM, buccal mucosa; TD, tongue dorsum; SupP, supraginval.

Figure 6

Functional characterization of the digestive microbiota based on metabolic pathway abundances in the buccal mucosa, supragingival plaque, tongue dorsum, and stool from metagenomic shotgun sequencing. Cladogram represents the KEGG BRITE functional hierarchy, with the outermost circles representing individual metabolic modules and the innermost very broad functional categories. Pathways coloration denotes modules showing significant differential abundances in at least one of the four body habitats. Metabolic profiling was performed with HUMAnN [48], revealing a much lower degree of variability among individuals and significant specifity of many pathways' relative abundance to individual body habitats. In particular, sugar transport and metabolism varies at each of the four habitats with metagenomic data, as does iron uptake and utilization.