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

By Nicola Segata, S. Haake, P. Mannon, K. P. Lemon, Levi Waldron, Dirk Gevers, Curtis Huttenhower, Jacques Izard. Genome Biology, 2012

991 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Periodontics

View Paper: https://www.semanticscholar.org/paper/336cc93154d842f77e2648427f1318b51df984a6

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Citations in the corpus

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences (2013, result): “Previous culture-based studies had detected higher frequencies of aerobic bacteria in the supragingival plaque relative to subgingival plaque 38 , and an analysis of HMP 16S rRNA sequences detected taxonomic differences between these two sites 39 .”
Relating the metatranscriptome and metagenome of the human gut (2014, background): “Although the oral and gut environments are anatomically linked, the degree of exchange between their resident microbiota is not completely understood (21).”
Chapter 12: Human Microbiome Analysis (2012, background): “Corynebacterium [116]), the oral cavity (dominated by Streptococcus) several hundred taxa (with remarkable diversity even among saliva, tongue, teeth, and other substrates [117,118]) and the gut over 500 taxa with densities over 10(11) cells/g [2,119].”
The composition of the gut microbiota shapes the colon mucus barrier (2014, positive): “The TM7 phylum is also found in human stool samples at low levels [47] and proposed to play a role in intestinal inflammation [48].”
Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor immune microenvironment (2013, background): “Our results demonstrate that Fusobacterium spp., rare gut microbiome constituents in the healthy human population (Segata et al., 2012), are found at increased abundance in the stool of patients with adenomas and colorectal cancer, and are enriched in adenomas and adenocarcinomas relative to…”
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible (2013, neutral): “…of “rarefying to even sampling depth” as a standard normalization procedure appears to explain why rareﬁed counts are also used in studies that attempt to detect differential abundance of OTUs between prede-ﬁned classes of samples [33–37], in addition to studies that use proportions directly [38].”
Compact graphical representation of phylogenetic data and metadata with GraPhlAn (2015, methodology): “This image has been generated by GraPhlAn using input files from the supporting “export2graphlan” script (see “Materials and Methods”) applied on the output of MetaPhlAn2 ( Segata et al., 2012 ) and LEfSe ( Segata et al., 2011 ).”
BugBase predicts organism-level microbiome phenotypes (2017, background): “Previous studies have shown distinct differences in the distribution of taxa within the stool and oral cavity, including an overall higher proportion of Firmicutes and Bacteroidetes in stool than in the oral cavity, and a higher proportion of Actinobacteria in plaque than on the tongue dorsum [17].”
Biogeography of a human oral microbiome at the micron scale (2016, background): “Bioinformatic analysis suggests that the genus Fusobacterium as a whole is substantially more abundant in subgingival than in supragingival plaque (20).”