Bacterial microbiota profiling in gastritis without Helicobacter pylori infection or non-steroidal anti-inflammatory drug use - PubMed (original) (raw)

Bacterial microbiota profiling in gastritis without Helicobacter pylori infection or non-steroidal anti-inflammatory drug use

Xiao-Xing Li et al. PLoS One. 2009.

Abstract

Recent 16S ribosomal RNA gene (rRNA) molecular profiling of the stomach mucosa revealed a surprising complexity of microbiota. Helicobacter pylori infection and non-steroidal anti-inflammatory drug (NSAID) use are two main contributors to gastritis and peptic ulcer. However, little is known about the association between other members of the stomach microbiota and gastric diseases. In this study, cloning and sequencing of the 16S rRNA was used to profile the stomach microbiota from normal and gastritis patients. One hundred and thirty three phylotypes from eight bacterial phyla were identified. The stomach microbiota was found to be closely adhered to the mucosa. Eleven Streptococcus phylotypes were successfully cultivated from the biopsies. One to two genera represented a majority of clones within any of the identified phyla. We further developed two real-time quantitative PCR assays to quantify the relative abundance of the Firmicutes phylum and the Streptococcus genus. Significantly higher abundance of the Firmicutes phylum and the Streptococcus genus within the Firmicutes phylum was observed in patients with antral gastritis, compared with normal controls. This study suggests that the genus taxon level can largely represent much higher taxa such as the phylum. The clinical relevance and the mechanism underlying the altered microbiota composition in gastritis require further functional studies.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1. The taxon tree for the stomach microbiota.

The tree was created based on the RDPII classifier based on a naive Bayesian rRNA classifier. The clone numbers for the top 5 phyla, top 6 classes, top 6 orders, top 7 families and top 10 genera were shown. Each taxon with at least 10 clones in all four sample groups (AGA, AGB, NmA, NmB) was analyzed by Pearson's chi-square test by comparing the clones numbers between AGA and AGB, NmA and NmB, AGA and NmA, and AGB and NmB. The clone numbers for all phylotypes were shown in Supplementary Figure S1.

Figure 2. Taxon-specific qPCR for quantifying abundance of a specific taxon within the stomach microbiota.

Two fluorescence probes (FAM and VIC) are located within the same PCR amplicon. The generic probe (VIC) targeting all bacteria sequences was used to quantify the total bacteria quantity. The taxon-specific probe (FAM) targeting to a specific taxon was used to quantify the quantity of the specific taxon. The taxon-specific probe matches perfectly to most species with the specific taxon, but has one or more mismatches to other species outside of the specific taxon. The ddCt value between VIC and FAM was used to quantify the abundance of the specific taxon.

Figure 3. Abundance of the Firmicutes phylum and the Streptoccous genus in different biopsies.

Delta delta Ct (ddCt) values (see text for details) were used to represent the abundance of the two taxa. A higher ddCt value represents a lower abundance of the taxon (abundance = 2−ddCt).

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Bacterial microbiota profiling in gastritis without Helicobacter pylori infection or non-steroidal anti-inflammatory drug use - PubMed (original) (raw)