Microbial diversity within the human stornach by cultUring and culture-independent methods

Abstract

This study was aimed to evaluate the microbial diversity of stomach samples (mucosa and gastric juice) from healthy humans by culturing and a phylogenetic metagenomic approach. Counts of were done in agar plates of non-selective rich media (Columbia Blood and Brain Heart Infusion) and in MRS with cysteine. Cultivable microorganisms of the gastric samples from different individuals ranged from 102 and 104 cfu/g. Representative isolates were identified at the species level by partial ARDRA and amplification, sequencing and comparison of their 16S rRNA genes. Sixteen bacterial species were identified among the cultures, a majority of which belonged to Propionibacterium acnes, Lactobacillus gasseri, and Staphylococcus epidermidis. Isolates would allow the selection of appropriate strains to be used as probiotics. Total microbial DNA purified from four mucosa samples was subjected to sequential nested PCR amplifications with 16S rDNA universal bacterial primers; amplicons were then pyrosequenced. A total of 15,659 high-quality, partial 16S rDNA reads larger than 200 nt were obtained. Sequence analysis grouped the reads into 59 families, 69 genera, and more than 300 OTUs (defined at a 97% of sequence identity). As in the cultures, notable differences in microbial numbers and types were observed between the subjects. However, the most abundant reads belonged in all four cases to Streptococcus, Propionibacterium and Lactobacillus species. Comparison of the stomach microbiota to that present in other parts of the human gastrointestinal tract showed distinctive microbial communities, that may be adapted to this harsh niche.