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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

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

Published: 14 June 2012

Additional files

Additional file 1:

Table s1 - average abundance, expressed in percentage of all microbial clades in the four digestive tract groups and among the ten body habitats. Lettering of groups and body habitats are as in Figure 1. AVG, average; STDEV, standard deviation.

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Additional file 2:

Table s2 - surfaces associated with the sampling sites from which the microbiota of the digestive tract was collected.

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Additional file 3:

Figure s1 - higher resolution version of Figure 1bshowing significantly enriched taxa from the four groups of digestive tract sites. This circular cladogram reports significant group-enriched taxa. Differential taxa analysis was performed using LEfSe on all the samples. Colored shading highlights which of the four major bacterial phyla was most enriched in which of the four body site groups. Each colored dot indicates a taxon that was differentially abundant among the groups. Small letters denote bacterial families that were enriched in one of the four body site groups.

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Additional file 4:

Figure s2 - diversity-based multidimensional scaling (MDS) plot of samples. A distance matrix for all pairwise distances between samples was calculated using Bray-Curtis distance, which was used to project samples to MDS coordinates using the stats::cmdscale R function with default options. Each of the four established groups of body sites (G1, G2, G3, G4) is assigned a color, decreasing in opacity as the density of points of that group decreases, and body sites are denoted with different marker types. G2 and G3 contain the most overlap, while maintaining distinct areas of highest density, while G1 and G4, respectively, increase in distinctness. The distribution of samples in specific body sites does not produce sub-clusters, confirming the homogeneity of bacterial community composition within the four groups.

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Additional file 5:

Table s3 - inverse Simpson for each habitat of the digestive tract. The minimum, maximum, average and standard deviation values are reported.

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Additional file 6:

Table s4 - percentages of subjects for whom each taxon was detected in both the upper digestive tract and in the stool. The table is ordered based on the absolute differences between the presence in the stool and in at least one oral body site. Only the subjects with samples in all ten digestive tract body habitats were considered (n = 147) and all the taxonomic units with at least 40% of presence in stool or any oral body site are included.

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Additional file 7:

Table s5 - read counts for all digestive tract samples (after quality control) for each microbial clade.

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Additional file 8:

Figure s3 - visual and schematic representation of the oral cavity and oropharyngeal sampling sites. The soft tissues, illustrated here in a 20-year-old healthy male, were sampled by swabbing the tongue dorsum, hard palate, right and left buccal mucosa, the anterior keratinized gingiva, the right and left palatine tonsils, and the throat (posterior wall of the oropharynx). The pooled supragingival and pooled subgingival plaque samples were taken with curettes from molars, premolars and incisors (schematic illlustration). Not shown is the sampling of the saliva, which was collected by having the subject drool accumulated saliva into a collection vial. The complete sampling procedure is described in the Manual of Procedures for Human Microbiome Project (see Materials and methods).

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Additional file 9:

Figure s4 - higher resolution version of Figure 6showing functional characterization of the digestive microbiota. Differentially abundant metabolic pathways from the buccal mucosa, supragingival plaque, tongue dorsum, and stool are depicted based on metabolic profiling performed with HUMAnN [48] from metagenomic shotgun sequencing data. Lettering indicates metabolic modules. Nucleot./amino acid met., nucleotide and amino acid metabolism; Carbohydrate/lipid met., carbohydrate and lipid metabolism; Energy met., energy metabolism; Met., aminoacyl tRNA and nucleotide sugar metabolism; Genetic information proc., genetic information processes; Environmental inf. proc., environmental information processing.

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Additional file 10:

Table s6 - percentages of metagenomic reads assigned to Archaea, Bacteria, and non-human Eukaryota (human reads excluded) in the four digestive tract sites with more than 50 shotgun sequencing samples available.

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Additional file 11:

Figure s5 - a subset of significant correlations between metagenomic gene family and organismal abundances. Paired shotgun metagenomic and 16S rRNA gene sequencing samples were associated, resulting in 34 buccal mucosa, 35 stool, 33 supragingival plaque, and 30 tongue microbiomes for joint analysis. Within each body site, Spearman correlations were calculated between the 21 KEGG Orthology gene families described in the Results and all phylotypes at any taxonomic level from phylum to OTU. Significant associations reaching a Benjamini-Hochberg false discovery rate <0.05 are shown here; grey ellipses represent clades, white rectangles KO gene families, and edge width is proportional to -log(q-value). Colors are as in Figure 1 (red, buccal mucosa; green, stool; yellow, plaque; blue, tongue).

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Additional file 12:

Table s7 - summary of the read statistics for 16S rRNA gene taxonomic abundances and whole genome shotgun sequencing metagenomic data.

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