Asian elephant (Elephas maximus) vaginal vestibule microbiomes are associated with reproductive hormones and physiology

Abstract Reproductive microbiomes are increasingly recognized as components of reproductive health, yet their relationships with reproductive physiology remain poorly understood across animal species. This is particularly relevant to endangered species, where reproductive dysfunction can constrain conservation breeding. Asian elephants ( Elephas maximus ) represent an important example, as reproductive acyclicity is prevalent in ex situ females and is associated with reduced fertility and welfare factors. Here, we characterized the vaginal vestibule (VV) microbiome of 13 ex situ Asian elephants using full-length 16S rRNA sequencing and examined associations with ovarian cyclicity, reproductive hormones, parity, age, and VV pH. VV microbiomes were taxonomically diverse, with abundant species including Porphyromonas somerae , P. canis , and Mycoplasmopsis equigenitalium . M. equigenitalium was enriched in low-progesterone states, including non-cycling females. Microbial diversity declined with age but increased with VV pH, with independent associations of both factors with diversity. Community composition differed between cycling and non-cycling females and was more similar between mother–calf pairs than unrelated individuals. Multiple bacterial taxa were associated with progesterone, parity, age, and VV pH. These findings identify reproductive physiology and ovarian cyclicity as important correlates of reproductive microbiome variation and provide a foundation for investigating microbiome–reproduction relationships relevant to conservation breeding in Asian elephants.