Clinical health issues, reproductive hormones, and metabolic hormones associated with gut microbiome structure in African and Asian elephants

BackgroundThe gut microbiome is important to immune health, metabolism, and hormone regulation. Captive animals provide an alternative approach to understand host-microbiome relationships and may lead to mediating long term health issues common in captive animals. Zoos strive to provide the best care to animals, yet animals often experience health issues. For instance, zoo managed African elephants (Loxodonta africana) and Asian elephants (Elephas maximus) experience low reproductive rates, high body condition, and gastrointestinal (GI) issues. We leveraged an extensive collection of fecal samples and health records from a large Elephant Welfare Project conducted across North American zoos in 2012 to examine the link between the gut microbiome and clinical health issues, reproductive hormones, and metabolic markers in captive elephants. We quantified gut microbiomes of 69 African and 48 Asian elephants from across 50 zoos using Illumina sequencing of the 16S rRNA bacterial gene.ResultsElephant species differed in microbiome structure, with African elephants having lower bacterial richness and dissimilar composition from Asian elephants. In both species, bacterial composition was strongly influenced by zoo facility. Bacterial richness was lower in African elephants with recent GI issues, and richness was positively correlated with metabolic hormone Total T3 in Asian elephants. In both elephant species, gut bacterial composition was associated with two metabolic hormones: free T4 and total T3. We found species-specific differences in relationships with other hormones such as fecal glucocorticoid metabolites (FGM) and luteinizing hormone (LH) in Asian elephants, and prolactin and progestagens in African elephants. We identified many relationships between bacterial relative abundances and hormone concentrations, including Prevotella spp., Treponema spp., and Akkermansia spp.ConclusionsWe present a comprehensive assessment of relationships between the gut microbiome, host species, environment, clinical health issues, and the endocrine system in captive elephants. Our results highlight the combined significance of host species-specific regulation and environmental effects on the gut microbiome between two elephant species and across 50 zoo facilities. We provide evidence of reproductive and metabolic hormones associated with gut bacterial composition and identified numerous bacterial taxa associated with concentrations of these hormones. Our findings establish the groundwork for future studies to investigate bacterial function or develop tools (e.g. prebiotics, probiotics, dietary manipulations) suitable for conservation and zoo management.