Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D et al.. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol 13: R42

Department of Molecular Genetics, 245 First Street, The Forsyth Institute, Cambridge, MA 02142, USA. .
Genome biology (Impact Factor: 10.81). 06/2012; 13(6):R42. DOI: 10.1186/gb-2012-13-6-r42
Source: PubMed


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.

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    • "The taxonomic cladogram shows a comparison between the MetaHIT and HMP studies limited to samples from the gut (for the latter) and from healthy subjects (for the former). 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). Colors distinguish between HMP (green) and MetaHIT (blue), while the intensity reflects the LDA score, an indicator of the effect sizes of the significant differences. "
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    ABSTRACT: The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization of very large-scale microbial and microbial community data paired with rich metadata. We developed GraPhlAn (Graphical Phylogenetic Analysis), a computational tool that produces high-quality, compact visualizations of microbial genomes and metagenomes. This includes phylogenies spanning up to thousands of taxa, annotated with metadata ranging from microbial community abundances to microbial physiology or host and environmental phenotypes. GraPhlAn has been developed as an open-source command-driven tool in order to be easily integrated into complex, publication-quality bioinformatics pipelines. It can be executed either locally or through an online Galaxy web application. We present several examples including taxonomic and phylogenetic visualization of microbial communities, metabolic functions, and biomarker discovery that illustrate GraPhlAn's potential for modern microbial and community genomics.
    PeerJ 06/2015; 3:e1029. DOI:10.7717/peerj.1029 · 2.11 Impact Factor
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    • "The keratinized mucosal surface present in the tongue dorsum is a distinct colonization surface relative to that of tooth structures, which are comprised of highly mineralized tissues such as enamel and cementum. Tooth surfaces are colonized by different consortia depending on the distinct anatomical site and gingival surfaces [31,32]. Not surprisingly, in our ordination plots using SupG, SubG, and tongue plaque, tongue samples clearly separated from tooth plaque samples (Figures 2 and 3A). "
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    08/2014; 2(32). DOI:10.1186/2049-2618-2-32
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    • "The human microbiome is a dynamic community changing in response to natural perturbations such as diet (Spencer et al., 2011; Turnbaugh et al., 2009; Wu et al., 2011; Zhang et al., 2010). The oral cavity of humans hosts several hundred taxa, with remarkable diversity even among saliva, tongue, teeth, and other substrates (Dewhirst et al., 2010; Segata et al., 2012). All of the surfaces of the mouth are covered in a bacterial biofilm (Wade, 2013). "
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