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. 2006 Jan 17;103(3):732-7.
doi: 10.1073/pnas.0506655103. Epub 2006 Jan 4.

Molecular Analysis of the Bacterial Microbiota in the Human Stomach

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Free PMC article

Molecular Analysis of the Bacterial Microbiota in the Human Stomach

Elisabeth M Bik et al. Proc Natl Acad Sci U S A. .
Free PMC article

Abstract

The microbiota of the human stomach and the influence of Helicobacter pylori colonization on its composition remain largely unknown. We characterized bacterial diversity within the human gastric mucosa by using a small subunit 16S rDNA clone library approach and analyzed 1,833 sequences generated by broad-range bacterial PCR from 23 gastric endoscopic biopsy samples. A diverse community of 128 phylotypes was identified, featuring diversity at this site greater than previously described. The majority of sequences were assigned to the Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria phyla. Ten percent of the phylotypes were previously uncharacterized, including a Deinococcus-related organism, relatives of which have been found in extreme environments but not reported before in humans. The gastric clone libraries from 19 subjects contained H. pylori rDNA; however, only 12 of these subjects tested positive for H. pylori by conventional laboratory methods. Statistical analysis revealed a large degree of intersubject variability of the gastric ecosystem. The presence of H. pylori did not affect the composition of the gastric community. This gastric bacterial rDNA data set was significantly different from sequence collections of the human mouth and esophagus described in other studies, indicating that the human stomach may be home to a distinct microbial eco-system. The gastric microbiota may play important, as-yet-undiscovered roles in human health and disease.

Figures

Fig. 1.
Fig. 1.
Phylogenetic tree with the 128 gastric 16S rDNA phylotype representatives from 23 human subjects. GenBank entries are shown in normal font; names of previously uncharacterized phylotype representatives (<99% sequence identity to published sequences) are shown in bold. Numbers of clones within each phylotype are shown in parentheses. The tree was constructed by neighbor-joining analysis by using an Olsen correction. Bootstrap values >50 (expressed as percentages of 100 replications) are shown at branch points. The scale bar represents evolutionary distance (10 substitutions per 100 nucleotides). The right side of the figure shows the relative abundance of phylotypes per gastric specimen in gray values (white, 0% present; black, 100% of clone library). Letters above the abundance graph correspond to subjects A–W in Table 3, which is published as supporting information on the PNAS web site. Subjects are grouped according to H. pylori status as determined by conventional and molecular tests, as indicated in Table 2, in increasing order of percentage of H. pylori clones.
Fig. 2.
Fig. 2.
Rarefaction analysis of the overall, combined bacterial 16S rRNA gene clone library recovered from human gastric biopsy specimens. The rarefaction curve, plotting the number of observed phylotypes (Sobs) as a function of the number of clones, was computed by estimates. The corrected Chao1 estimator for species richness (after 1,000 randomizations) was plotted as well. The dotted lines indicate the 95% confidence interval.
Fig. 3.
Fig. 3.
Relative phylotype frequencies of clones isolated from gastric specimens. Sequences were assigned to a bacterial phylum according to their position in the phylogenetic tree in Fig. 1. Σ, combined libraries from all 23 subjects, including H. pylori sequences (1,833 sequences). Gastric libraries were divided into three groups; members are defined in Fig. 1 and Table 3. Groups: 1, clone libraries not containing H. pylori rDNA sequences from four subjects negative for H. pylori by conventional testing; 2, clone libraries containing H. pylori sequences from seven subjects negative for H. pylori by conventional testing; 3, clone libraries containing H. pylori sequences from 12 subjects positive for H. pylori by conventional testing. For groups 1–3, only non-H. pylori sequences are shown.

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