Identification of shared bacterial strains in the vaginal microbiota of reproductive-age mothers and daughters using genome-resolved metagenomics

Abstract

It has been suggested that the human microbiome might be vertically transmitted from mother to offspring and that early colonizers may play a critical role in development of the immune system. Studies have shown limited support for the vertical transmission of the intestinal microbiota but the derivation of the vaginal microbiota remains largely unknown. Although the vaginal microbiota of children and reproductive age cis women differ in composition, the vaginal microbiota could be vertically transmitted. To determine whether there was any support for this hypothesis, we examined the vaginal microbiota of daughter-mother pairs from the Baltimore metropolitan area (ages 14-27, 32-51; n=39). We assessed whether the daughter’s microbiota was similar in composition to their mother’s using metataxonomics. Permutation tests revealed that while some pairs did have similar vaginal microbiota, the degree of similarity did not exceed that expected by chance. Genome-resolved metagenomics was used to identify shared bacterial strains in a subset of the families (n=22). We found a small number of bacterial strains that were shared between mother-daughter pairs but identified more shared strains between individuals from different families, indicating that vaginal bacteria may display biogeographic patterns. Earlier-in-life studies are needed to demonstrate vertical transmission of the vaginal microbiota.ImportanceEarly colonizers of our microbiota are theorized to play an important role in the development of our immune system, yet we know little about how these communities are established. Vertical transmission from mother to offspring at the time of birth is theorized to be a major source of early colonizers but limited evidence supporting this process has only been shown for the intestinal tract microbiota. The provenance of the vaginal microbiota is largely unknown, although some have posited it is similarly vertically transmitted. We examined the vaginal microbiota of mother-daughter pairs and found limited evidence in support of this hypothesis. However, our analysis also revealed putative biogeographic patterns in the distribution of the strains which comprise the vaginal microbiota. Our results give insight into the role of vertical transmission for the vaginal microbiota and motivate future studies on the biogeography of these bacteria.

Persistence and In Vivo Evolution of Vaginal Bacterial Strains over a Multiyear Time Period

“…We next sought to determine which participants had maintained the same strain(s) over the 1- to 2-year time period. De novo assembly using metaSPAdes ( 15 ) and contig binning, as described previously ( 16 ), produced 53 metagenome assembled genomes (MAGs), representing 15 species ( Fig. 1B ).…”

Persistence andin vivoevolution of vaginal bacterial strains over a multi-year time period

“…We next sought to determine which participants had maintained the same strain(s) over the 1-2-year time period. De novo assembly using metaSPAdes (14) and contig binning, as described previously (15), produced 53 metagenome assembled genomes (MAGs), representing 15 species ( Figure 1B ). To identify which participants had the same strain(s) at the two timepoints, we used inStrain (16), with a percent identify threshold of at least 99.9%.…”