Contrasting diversity of vaginal lactobacilli among the females of Northeast India

BACKGROUND: Lactobacilli are gatekeepers of vaginal ecosystem impeding growth of pathogenic microbes and their diversity varies across populations worldwide. The present study investigated diversity of human vaginal microbiota among females of Northeast India, who are distinct in dietary habits, lifestyle, and genomic composition from rest of India. RESULTS: Altogether, 154 bacterial isolates were obtained from vaginal swab samples of 40 pregnant and 29 non-pregnant females. The samples were sequenced for 16 s rRNA gene and analysed for identification using a dual approach of homology search and maximum likelihood based clustering. Molecular identification based on 16S rRNA gene sequence confirmed the isolates belonging to 31 species. Lactobacilli constituted 37.7% of the bacterial isolates with 10 species and other Lactic Acid Bacteria (39.61%) represented another 10 species, some of which are opportunistic pathogens. The remaining of the communities are mostly dominated by species of Staphylococcus (14.28%) and rarely by Propionibacterium avidum (3.90%), Bacillus subtilis, Escherchia coli, Janthinobacterium lividum, and Kocuria kristinae (each 0.64%). Interestingly Lactobacillus mucosae and Enterococcus faecalis, which are globally uncommon vaginal microbes is found dominant among women of Northeast India. This tentatively reflects adaptability of particular Lactobacillus species, in distinct population, to better compete for receptors and nutrients in vaginal epithelium than other species. Further, intrageneric 16S rRNA gene exchange was observed among Enterococcus, Staphylococcus, and two species of Lactobacillus, and deep intraspecies divergence among L. mucosae, which pinpointed possibility of emergence of new strains with evolved functionality. Lactobacilli percentage decreased from young pregnant to aged non-pregnant women with maximum colonization in trimester II. CONCLUSION: The study highlighted importance of assessment of vaginal microbiota, Lactobacillus in particular, across different population to gain more insight on female health. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12866-019-1568-6) contains supplementary material, which is available to authorized users.