Host-associated microbial communities (“microbiomes”) play a critical role in influencing a diverse suite of whole-organism functions, with classic examples including immunity and metabolism. probiotics) or indirectly via dietary manipulation or prebiotics. Further work is required to understand the efficacy and feasibility of this, either directly through microbial augmentation (e.g. We identified four genera that were associated with multiple indicators of reproductive output these could be candidate probiotics to improve the breeding success of black rhino in zoo-based conservation breeding programmes. Although the directionality of the relationship is unclear, the variation in gut microbiome communities represents a potential biomarker of reproductive health. Our results indicate that many members of the gut microbiome of black rhino are associated with hormone production and breeding success, and some members of the rare microbiota appear to be particularly important. These genera had a lower-than-average relative abundance in the gut microbiome. Through a combination of analyses, we identified four genera ( Aerococcaceae, Atopostipes, Carnobacteriaceae and Solobacterium) that were significantly associated with breeding success, pregnancy and/or post-parturition, and higher faecal progestagen metabolite concentrations. Around a third of bacterial genera showed more than ± 10% correlation with either progestagen and/or glucocorticoid concentration, and in general, microbial genera correlated with both hormones in the same direction. In particular, the gut microbiome during pregnancy and post-parturition was significantly altered. We identified significant differences in black rhino gut microbiome composition according to ID, institution, breeding success and ovarian cycle phase. Here, we characterise faecal bacterial communities of breeding and non-breeding eastern black rhino ( Diceros bicornis michaeli) using 16S rRNA gene amplicon sequencing and quantify progestagen and glucocorticoid metabolite concentrations through enzyme immunoassays to identify such relationships. This is of particular relevance to species in zoo-based conservation breeding programmes, as relationships between host microbiome composition and reproductive output may allow for the development of microbial augmentation strategies to improve success. Host microbiomes play a role in hormone production and subsequent fertility in humans, but this is less well understood in non-model organisms.
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