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Commensal Microbiota and Reproductive Health in Livestock: Mechanisms, Cross-System Crosstalk, and Precision Strategies
by
,
Xiaohan Zhou
1,
Jinping Cao
1,
Guanghang Feng
1,
Yaokun Li
1,2,
Dewu Liu
1,2,* and
Guangbin Liu
1,2,* 1
College of Animal Science, South China Agricultural University, Guangzhou 510642, China
2
National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
*
Authors to whom correspondence should be addressed.
Animals 2026, 16(3), 371; https://doi.org/10.3390/ani16030371
Submission received: 24 December 2025
/
Revised: 17 January 2026
/
Accepted: 21 January 2026
/
Published: 23 January 2026
(This article belongs to the Section Small Ruminants)
Simple Summary
Reproductive performance is fundamental to the success and sustainability of the livestock industry. While traditional efforts have centered on genetics and hormones, it is now clear that the vast communities of bacteria within an animal, known as the microbiome, are vital to reproductive health. This review explores the “gut-reproductive axis” and explains how these microorganisms transmit chemical signals from the digestive tract to reproductive organs. We examine how microbial communities impact fertility and pregnancy in cattle, pigs, sheep, and poultry. Understanding these links allows the industry to adopt more effective breeding and health management strategies, such as using probiotics or artificial intelligence to improve the efficiency of food production.
Abstract
Reproductive performance in livestock and poultry is a core determinant of economic efficiency in the animal industry. While traditional research has primarily focused on genetics, endocrinology, and immune regulation, emerging microbiome studies reveal that commensal microbiota within the gut and reproductive tracts play an underestimated yet pivotal role in host reproductive health. This review systematically synthesizes recent advances regarding the relationship between the microbiome and reproductive functions in major livestock species (cattle, pigs, sheep, and chickens). We first delineate the theoretical basis and mechanisms of the “gut-reproductive axis,” highlighting cross-system communication mediated by microbial metabolites, including short-chain fatty acids (SCFAs), indoles, and bile acids. Subsequently, we provide an in-depth comparative analysis of the microecological features of both female (vagina/uterus) and male (semen/epididymis) reproductive systems, examining their impacts on fertility, sperm quality, and pregnancy outcomes. Furthermore, we explore the molecular and systemic mechanisms governing microbial regulation of reproduction, encompassing the modulation of the hypothalamic-pituitary-gonadal (HPG) axis, the balance of local mucosal immunity and inflammation, and epigenetic regulation. Finally, we address current challenges—such as causal validation and the scarcity of multi-species databases—and propose future directions, including spatial multi-omics, AI-integrated analysis, and microbial intervention strategies. Ultimately, this review aims to offer a theoretical foundation and translational insights for elucidating reproductive regulatory networks and developing microbiome-driven precision strategies to enhance reproductive performance.
