Multi‐omics analysis of gut‐organ axes reveals the high‐altitude adaptation in Tibetan chicken

Abstract The Qinghai‐Tibet Plateau is an extreme ecosystem subject to special climatic conditions that require unique adaptations for its inhabiting organisms. In addition to genetic characteristics, the gut microbiota of animals can regulate the environmental adaptation of their hosts through various gut–organ axes. We performed a multi‐omics analysis on six Chinese chicken populations based on geographical differences in altitude: one high‐altitude Tibetan chicken population, one transitional Tibetan chicken population relocated from high to low altitude, and four low‐altitude populations. We found significant differences in gut microbiota among these different chicken populations, which were governed by variations in habitat species pools and turnover, indicating a more complex and stochastically dominated gut microbiota with higher functional redundancy in the Tibetan chicken population under the plateau environment. Furthermore, Tibetan chickens had a more effective fatty acid degradation capacity, corresponding to the hypoxic environment. In contrast, chickens living in lowland environments showed stronger immune system responses against health threats. These environmental adaptation strategies are regulated by core gut microbe taxa of the phylum Firmicutes. Thus, our findings demonstrate the roles of breed and habitat in gut microbiota composition of chickens and clarify their adaptation strategies to environmental changes via microbiota‐driven gut–organ axes.