Comparative metagenomic analysis of diarrheal and non-diarrheal gut microbiome delineating the prospective development of prognostic markers and probiotics to protect from diarrhea

Abstract

A cross-sectional gut microbiome analysis of 23 non-diarrheal and 5 diarrheal fecal samples was conducted by employing 16s rRNA amplicon sequencing and subsequent analysis for taxonomic profiling of OTUs and abundance interpretation of reads. Significant differences in the structural composition of the two groups were observed. In both Firmicutes was the most abundant phylum in majority of the samples. B/F ratio was consistently <1 in all diarrheal samples. Significant difference in mean B/F ratio of the two groups was found. Proteobacteria was significantly more abundant in the diarrheal group. Prevotellaceae was the most abundant family in non-diarrheal samples and was suppressed significantly in diarrheal samples. Streptococcaceae was the most abundant family in 60% diarrheal samples and where Streptococcaceae was suppressed, Bacteroideaceae and Nocardeaceae were the most abundant. In non-diarrheal samples where Streptococcaceae was almost completely suppressed Bifidobacteriaceae was the most abundant and suppressed other families significantly. A negative correlation was observed between Prevotellaceae and Bacteroideaceae in the non-diarrheal group. Prevotella copri was the most abundant species in 70% non-diarrheal samples and was significantly suppressed in diarrheal samples. Proteus mirabilis was identified in all the non-diarrheal samples while they were absent in diarrheal samples. The OTUs associated with diarrheal dysbiosis can serve as prognostic markers. This is the first report on the comparative analysis of diarrheal and non-diarrheal microbiome, to our knowledge, and distinctly addressing the gut microbiome dysbiosis from the context that can lead to the development of prognostic markers and probiotics for protecting the endemic population from diarrhea.