Background The gut microbiome is important to immune health, metabolism, and hormone regulation. Understanding host–microbiome relationships in captive animals may lead to mediating long term health issues common in captive animals. 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 the Elephant Welfare Study conducted across North American zoos in 2012 to examine the link between gut microbiota and clinical health issues, reproductive hormones, and metabolic hormones 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. Results Elephant species differed in microbiome structure, with African elephants having lower bacterial richness and dissimilar bacterial 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 triiodothyronine (total T3) in Asian elephants. We found species-specific associations between gut microbiome composition and hormones: Asian elephant gut microbiome composition was linked to total T3 and free thyroxine (free T4), while fecal glucocorticoid metabolites (FGM) were linked to African elephant gut microbiome composition. We identified many relationships between bacterial relative abundances and hormone concentrations, including Prevotella spp., Treponema spp., and Akkermansia spp. Conclusions We 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 clinical health issues, reproductive hormones, and metabolic hormones associated with the gut microbiome structure of captive elephants. 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.

In mammalian neonates, milk consumption provides nutrients, growth factors, immune molecules, and microbes. Milk microbiomes are increasingly recognized for their roles in seeding infant gut microbiomes and priming immune development. However, milk microbiome variation within and among individuals remains under investigation. We used 16S rRNA gene sequencing to investigate factors shaping milk microbiomes in three captive great ape species: Gorilla gorilla gorilla (individuals, N = 4; samples, n = 29), Pongo abelii (N = 2; n = 16), and Pongo pygmaeus (N = 1; n = 9). We demonstrate variation among host species, over lactation, and between housing facilities. In phylogenetic community composition, milk microbiomes were distinct among the three ape species. We found only a few shared, abundant bacterial taxa and suggest that they likely serve functional roles. The diversity and community composition of milk microbiomes showed gradual changes over time in gorillas and the Bornean orangutan, which was detectable with our comprehensive sampling over lactation stages (> 300-day span). In gorillas, milk microbiomes differed between housing facilities, but were similar between dams within a facility. These results support the strong influence of evolutionary history in shaping milk microbiomes, but also indicate that more proximate cues from mother, offspring, and the environment affect the distribution of rarer microbial taxa.