Characterizing the human vaginal microbiome using high-throughput sequencing

The human vaginal microbiome undoubtedly has a significant role in reproductive health and for protection from infectious organisms. Recent efforts to characterize the bacterial species of the vagina using molecular techniques have uncovered an unexpected diversity. Using high-throughput sequencing I sought to describe the structure and function of the vaginal microbiome under different physiological states including healthy, bacterial vaginosis (BV), post-menopausal vaginal atrophy, and acute vulvovaginal candidiasis (VVC). Partial 16S rRNA gene sequencing revealed that healthy, asymptomatic women most often have vaginal biotas dominated by Lactobacillus iners or L. crispatus. In contrast, BV is a heterogeneous, highly diversified condition with reduced Lactobacillus abundance. Similar to BV, post-menopausal women experiencing vaginal dryness were depleted in lactobacilli and had a more diverse vaginal profile. In the case of VVC, the biotas were not significantly altered compared to healthy women despite the fungal overgrowth. One organism, Lactobacillus iners was ubiquitously present in all conditions, and became predominant following antibiotic and probiotic treatment of BV. To uncover the potential role of this bacterium, I used whole genome sequencing of vaginal isolate AB-1. The genome is predicted to be the smallest of any Lactobacillus at 1.3 Mbp, but having a higher proportion of horizontally acquired genes. These results, along with predicted adhesins and a cholesterol-dependent cytolysin, indicate L. iners is highly adapted for the vagina and could have an uncharacterized role in the etiology of BV. As BV is the most common vaginal ailment with severe implications on acquisition and transmission of sexually transmitted infections, and complications during pregnancy, I sought iito examine the functional contribution of the organisms during BV using meta-RNA sequencing. L. iners drastically modulates gene expression in response to BV, and notably increases expression of a cholesterol-dependent cytolysin, mucin and glycerol transport and metabolic enzymes, and genes belonging to a CRISPR system - suggestive of bacteriophage influence in the community. Although diverse in taxonomic membership, there is evidence of functional conservation in BV including preference for glycogen and glycerol as carbon sources, and predicted end products of metabolism including an abundance of succinate and short-chain fatty acids. These studies add significantly to our understanding of the role lactobacilli can play in vaginal and reproductive health

Microbiota at Multiple Body Sites during Pregnancy in a Rural Tanzanian Population and Effects of Moringa-Supplemented Probiotic Yogurt

The nutritional status of pregnant women is vital for healthy outcomes and is a concern for a large proportion of the world's population. The role of the microbiota in pregnancy and nutrition is a promising new area of study with potential health ramifications. In many African countries, maternal and infant death and morbidity are associated with malnutrition. Here, we assess the influence of probiotic yogurt containing Lactobacillus rhamnosus GR-1, supplemented with Moringa plant as a source of micronutrients, on the health and oral, gut, vaginal, and milk microbiotas of 56 pregnant women in Tanzania. In an open-label study design, 26 subjects received yogurt daily, and 30 were untreated during the last two trimesters and for 1 month after birth. Samples were analyzed using 16S rRNA gene sequencing, and dietary recalls were recorded. Women initially categorized as nourished or undernourished consumed similar calories and macronutrients, which may explain why there was no difference in the microbiota at any body site. Consumption of yogurt increased the relative abundance of Bifidobacterium and decreased Enterobacteriaceae in the newborn feces but had no effect on the mother's microbiota at any body site. The microbiota of the oral cavity and GI tract remained stable over pregnancy, but the vaginal microbiota showed a significant increase in diversity leading up to and after birth. In summary, daily micronutrient-supplemented probiotic yogurt provides a safe, affordable food for pregnant women in rural Tanzania, and the resultant improvement in the gut microbial profile of infants is worthy of further study