Reproductive hormones mediate changes in the gut microbiome during pregnancy and lactation in Phayre’s leaf monkeys

Studies in multiple host species have shown that gut microbial diversity
and composition change during pregnancy and lactation. However, the
specific mechanisms underlying these shifts are not well understood. Here,
we use longitudinal data from wild Phayre’s leaf monkeys to test the
hypothesis that fluctuations in reproductive hormone concentrations
contribute to gut microbial shifts during pregnancy. We described the
microbial taxonomic composition of 91 fecal samples from 15 females (n=16
cycling, n=36 pregnant, n=39 lactating) using 16S rRNA gene amplicon
sequencing and assessed whether the resulting data were better explained
by overall reproductive stage or by fecal estrogen (fE) and progesterone
(fP) concentrations. Our results indicate that while overall reproductive
stage affected gut microbiome composition, the observed patterns were
driven by reproductive hormones. Females had lower gut microbial diversity
during pregnancy and fP concentration was negatively correlated with
diversity. Additionally, fP concentration predicted both unweighted and
weighted UniFrac distances, while reproductive state only predicted
unweighted UniFrac distances. Seasonality (rainfall and periods of
phytoprogestin consumption) additionally influenced gut microbial
diversity and composition. Our results indicate that reproductive
hormones, specifically progestagens, contribute to the shifts in the gut
microbiome during pregnancy and lactation.