Bacterial community shifts in geriatric subjects in response to probiotic intervention revealed by high throughput DNA sequencing
Evidences on the association between bacterial shifts in human gut microbiota and disorders such as inflammatory bowel disease, diabetes and obesity are mounting. A comprehensive catalogue of gut microbiota is thus essential for personalized microbiome focused treatments. The microbiota of older people displays greater inter-individual variation than that of younger adults. Gastrointestinal disorders are a major cause of morbidity in the geriatric population. Probiotic interventions are known to have been shown to inﬂuence the composition of the intestinal microbiota in the geriatric. As most of the bacteria present in the gut are non culturable, we attempted to study the bacterial community structure of the geriatric gut using Ion torrent 16s rRNA seqeuencing. There remains considerable variability in response to probiotic intervention among subjects, hence we hypothesized that a signature gut metagenome could be the deciding biomarker for a successfully probiotic therapy. Among the 72 geriatric subjects who participated in the trial, we could identify 10 respondents who showed positive results in the primary outcome of cholesterol reduction and 10 who showed an increase in cholesterol with a decreasing lactobacilli population indicating non response to probiotic therapy. DNA from the faecal samples of these 20 respondents during baseline and end of feeding was analyzed. Amplicons from the hypervarialbe region of the 16S rRNA gene were generated and sequenced each on a 316 chip. Sequencing reads were clustered into operational taxonomic units described by community metrics and taxonomically classified. Reads per sample were clustered and studied for diversity and richness using MG-RAST. All the community members in our samples were from the domain bacteria. The most prevalent phyla in all samples were: Firmicutes, Proeobacteria, Actinobacteria and Bacteroidetes with Firmicutes dominating in all samples. All the samples taken prior to treatment showed an abundance in Blautia, Bifidobacterium, clostridium, Escherichia, Eubacterium, Faecalibacterium, Lactobacillus, Prevotella, Roseburia, Ruminococcus and Shigella. It was strikingly evident that the non respondents harboured more Shigella, Escherichia and less Runinococcus and Clostridium (compared to positive respondents). Lactobacilli and Prevotella showed an increase in abundance values after probiotic treatment with a decrease in Shigella, Ruminococcus, Bacillus and Bifidobacterium. Such metagenomic analysis gives new insights into differences in response towards the same probiotic intervention due to host community profiles. Modulation of the community structure using probiotics can prove beneficial for geriatric intestinal well-being and cholesterol reduction.
Keywords: Metagenome, Probiotic gut, Geriatric