Description
Strain-level variation in the microbiome of the female genital tract
Matthew R. Hayward1, Seth M. Bloom1,2, Nomfuneko A. Mafunda1, Jiawu Xu1, Brittany A. Bowman1, Christina Gosmann1, Bjorn Corleis1, Mara Farcasanu1, Justin K. Rice1, Curtis Huttenhower2,3, Caroline M. Mitchell2 and Douglas S. Kwon1,2
1Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; 2Massachusetts General Hospital, Boston, MA, USA; 3The Broad Institute of MIT and Harvard, Cambridge, USA
The microbes colonising the female genital tract (FGT) influence multiple health outcomes including preterm birth, HIV acquisition and baseline inflammation. Most studies have profiled the microbiome through bacterial 16S rRNA gene sequencing; though informative, 16S-based taxonomic classification is limited to species-level resolution. Within-species genetic differences can be vast, with some species-level pangenomes (all the unique genes seen for a species) exceeding the size of any single strain's genome by orders of magnitude. Furthermore, 16S sequencing provides no functional information; placing a limit on our mechanistic understanding of disease associations.
To better characterize strain-level associations with major reproductive stages (pre-menopause, pregnancy, and post-menopause), BV and geography we sequenced 1000 primary bacterial isolates and generated shotgun metagenomes for 500 samples from North America and South Africa. We combined these data with >1800 curated reference genomes and >1000 publicly available metagenomic sequences. By integrating species-specific pangenomes and shotgun metagenomes we were able to assemble strain-level gene profiles. Profiles were partitioned using centroid based clustering to form strain-level groups containing similar gene complements. Functional annotation of the genes in these groups was used to identify potential strain-level phenotypes which differ between the FGT microbiome under different conditions.
We show that most FGT species possess a small core genome (~1000 genes) with an extensive pangenome (6000 to 30,000 genes) that varies between strains and encodes diverse metabolic functions. We show that some women are colonised by sub-species complexes (multiple distinct strains of the same species). We determine which strains form these complexes and relate them to primary isolates. These findings open avenues for mechanistic studies between the FGT microbiome and the reproductive health of the host.