Vaginal microbiome composition drives metabolic profiles in healthy pregnancy
Early life exposure to microbes may be critical to healthy infant development yet this process remains poorly characterized. An infant begins physiologically responding to microbes in utero and during birth, when she or he is exposed to maternal microbes and metabolic products. However, it is unclear to what extent the infant metabolome is molded by the microbiome and metabolome of its mother. Vaginal microbial communities are relatively simple communities, typically dominated by one or a few microbes, which are able to survive in a narrow pH range. In this study, we characterized the vaginal microbiomes and metabolomes of eighteen women throughout three trimesters of pregnancy and the metabolomes of their offspring through the first year of life. 16S rDNA and ITS amplicon sequencing revealed simple communities dominated by Lactobacillus sp. and more diverse communities characterized by a high abundance of Gardnerella. Integrating GCMS and LCMS metabolomic data with amplicon sequencing, we found several metabolites that were associated with particular communities. For example, mannitol and indole-3-lactate were highly correlated with the presence of Lactobacillus crispatus. Metabolites that were only detected in a particular community type, which could be useful biomarkers, may indicate orthogonal approaches to metabolize available carbon sources. Additional sequence data from shotgun metagenomics improved the resolution of taxonomy established by amplicon sequencing, and found functional genes involved in microbial metabolism. Genomic analysis confirmed that many identified metabolic products could be processed or produced by the microbial communities present. By utilizing additional –omics data, we provide a more encompassing view of functional aspects of the maternal microbiome, which could someday influence therapies that lead to healthier outcomes for both mother and child.