Bacterial biogeography of the human digestive tract

Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
Scientific Reports (Impact Factor: 5.58). 11/2011; 1:170. DOI: 10.1038/srep00170
Source: PubMed


We present bacterial biogeography as sampled from the human gastrointestinal tract of four healthy subjects. This study generated >32 million paired-end sequences of bacterial 16S rRNA genes (V3 region) representing >95,000 unique operational taxonomic units (OTUs; 97% similarity clusters), with >99% Good's coverage for all samples. The highest OTU richness and phylogenetic diversity was found in the mouth samples. The microbial communities of multiple biopsy sites within the colon were highly similar within individuals and largely distinct from those in stool. Within an individual, OTU overlap among broad site definitions (mouth, stomach/duodenum, colon and stool) ranged from 32-110 OTUs, 25 of which were common to all individuals and included OTUs affiliated with Faecalibacterium prasnitzii and the TM7 phylum. This first comprehensive characterization of the abundant and rare microflora found along the healthy human digestive tract represents essential groundwork to investigate further how the human microbiome relates to health and disease.

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Available from: Dilani B Senadheera
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    • "The human large intestine is a dynamic microbial ecosystem inhabited by different bacterial species, which reach their highest concentrations in the colon (up to 10 12 cells per gram of feces) (Doré & Corthier, 2010). In adults, Bacteroidetes (including Bacteroides and Prevotella genera) and Firmicutes (including Clostridium, Enterococcus, Lactobacillus, Faecalibacterium and Ruminococcus genera) phyla predominated in colon mucosal sites, whereas proteobacteria, fusobacteria, actinobacteria, and verrucomicrobia are in considerably minor proportion (Qin et al., 2010; Stearns et al., 2011). Although the colonic microbiota is relatively stable throughout adult life, age-related changes in the gastrointestinal (GI) tract, inter-individual differences, as well as dietary factors and diverse disease conditions, inevitably affect population composition changing its microbial and metabolic profiles (Salonen & De Vos, 2014). "
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    ABSTRACT: Polyphenols present in wine may favorably influence human health by means of modifying the metabolic activity and /or composition of gut microbiota. The aim of this study was to evaluate the impact of red wine on colonic metabolism using a novel Dynamic Gastrointestinal Simulator (namely SIMGI), inoculated with human feces of healthy volunteers (n=2). Main wine phenolic compounds and their metabolites, ammonium and short-chain fatty acids (SCFAs) as well as main microbial groups were monitored in samples from the three colon compartments – ascending, transverse and descending – after feeding the system with red wine (225 mL). Significant increases were found for gallic acid, protocatechuic acid, 3-O-methylgallic acid, 4-hydroxybenzoic, 3,4-dihydroxyphenylpropionic acid, vanillic acid, syringic acid and salicylic acid after wine feeding. Concurrently, a decrease in ammonium ion and an increase in the proportion of butanoic acid were observed. In turn, the microbiota metabolic activity was found different between the two individuals and among the three compartments, with the main changes occurring in the ascending colon. These results highlight that red wine modulates the metabolic activity of colonic microbiota in vitro, which could be physiologically relevant, and contribute to our understanding on the complex metabolic fate of dietary polyphenols and polyphenols-microbiota interactions.
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    • "Bacterial communities that colonize the human body are intimately linked with host physiology, immunity, metabolism, and nutrition [1-3]. Of colonization sites, the mouth accommodates a bacterial consortium with high taxonomic richness and phylogenetic diversity [4-6]. The microbial composition of the plaque biofilm has a critical role in oral health. "
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    ABSTRACT: Background: Periodontitis is an infectious and inflammatory disease of polymicrobial etiology that can lead to the destruction of bones and tissues that support the teeth. The management of chronic periodontitis (CP) relies heavily on elimination or at least control of known pathogenic consortia associated with the disease. Until now, microbial plaque obtained from the subgingival (SubG) sites has been the primary focus for bacterial community analysis using deep sequencing. In addition to the use of SubG plaque, here, we investigated whether plaque obtained from supragingival (SupG) and tongue dorsum sites can serve as alternatives for monitoring CP-associated bacterial biomarkers. Results: Using SubG, SupG, and tongue plaque DNA from 11 healthy and 13 diseased subjects, we sequenced V3 regions (approximately 200 bases) of the 16S rRNA gene using Illumina sequencing. After quality filtering, approximately 4.1 million sequences were collapsed into operational taxonomic units (OTUs; sequence identity cutoff of >97%) that were classified to a total of 19 phyla spanning 114 genera. Bacterial community diversity and overall composition was not affected by health or disease, and multiresponse permutation procedure (MRPP) on Bray-Curtis distance measures only supported weakly distinct bacterial communities in SubG and tongue plaque depending on health or disease status (P?<?0.05). Nonetheless, in SubG and tongue sites, the relative abundance of Firmicutes was increased significantly from health to disease and members of Synergistetes were found in higher abundance across all sites in disease. Taxa indicative of CP were identified in all three locations (for example, Treponema denticola, Porphyromonas gingivalis, Synergistes oral taxa 362 and 363). Conclusions: For the first time, this study demonstrates that SupG and tongue dorsum plaque can serve as alternative sources for detecting and enumerating known and novel bacterial biomarkers of CP. This finding is clinically important because, in contrast with SubG sampling that requires trained professionals, obtaining plaque from SupG and tongue sites is convenient and minimally-invasive and offers a novel means to track CP-biomarker organisms during treatment outcome monitoring.
    Full-text · Article · Aug 2014
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    • "Few studies have analyzed the composition of the human gastric microbiota in healthy individuals and in patients suffering from different diseases. These studies used high-throughput molecular approaches including metagenomics [15] [16] [17] [18], terminal restriction fragment length polymorphism (T-RFLP) [19], and microarray [20] that are powerful techniques that enable the capture of DNA sequences from most of the bacteria present in the stomach including both culturable and nonculturable species. However, one important limitation in these studies is the small number of human samples (4–23 individuals) making it difficult to generate statistically significant conclusions. "
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