Molecular analysis of the bacterial microbiota in the human stomach

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 ecosystem. The gastric microbiota may play important, as-yet-undiscovered roles in human health and disease.

Structure of the human gastric bacterial community in relation to Helicobacter pylori status

“…Consistent with previous studies (Bik et al, 2006;Andersson et al, 2008), the human gastric bacterial community is very rich but uneven, strongly dominated by only four phyla, namely, Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria.…”

“…In addition to H. pylori, the stomach can also contain transient oral, esophageal or intestinal bacteria. To date, the few studies that have explored the microbiota of the human stomach using molecular methods (Bik et al, 2006;Andersson et al, 2008) have shown that the gastric community is highly dominated by Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes, with H. pylori being the single dominant bacteria in patients of positive H. pylori status. Bik et al (2006) sequenced 1833 bacterial clones from gastric biopsy samples from 23 US patients and found eight bacterial phyla (128 phylotypes) with no differences in richness by H. pylori status and with 7 of 11 patients of apparent negative H. pylori status having H. pylori clones.…”

Gastrointestinal microorganisms in cats and dogs: a brief review

“…Despite this diversity, one single genus (i.e., Helicobacter) was by far the most predominant (~ 98% of all gastric microbiota). These results are in accordance with one study that showed that the human stomach is also home of a diverse microbiota, although the genus Helicobacter (H. pylori only) constituted only 42% of all sequences analyzed (Bik et al 2006).…”

Association between living environment and human oral viral ecology

“…The study of the human microbiome focuses predominantly on bacterial flora (Bik et al, 2006;Gao et al, 2007;Costello et al, 2009); however, there are numerous reports of viral communities inhabiting different body sites (Bachrach et al, 2003;Breitbart et al, 2003;Bik et al, 2006;Gao et al, 2007;Breitbart et al, 2008;Costello et al, 2009;Reyes et al, 2010). Although there are viruses of Eukarya inhabiting these sites (Victoria et al, 2009;Foulongne et al, 2012;Lysholm et al, 2012), the majority of the viruses that have been identified in these habitats are bacteriophage (Breitbart et al, 2008;Willner et al, 2009).…”