Multi-omics analysis of gut-organ axes reveals the environmental adaptation mechanisms in Tibetan chicken

Abstract Background As a representative extreme ecosystem, the Qinghai-Tibet Plateau is subject to special climatic conditions, that require unique adaptations for organisms living in the region. In addition to genetic characteristics, the gut microbiota in animals can regulate the environmental adaptation of hosts through various "gut-organ" axes. The Tibetan chicken is the principal poultry species raised on the Qinghai-Tibet Plateau, however there is limited understanding of the interactions of its gut microbiota and host gene expression, as well as their associations with the plateau’s hypoxic conditions. In this study, a multi-omics approach was used to investigate the gut microbiota of Tibetan chickens and to explore the environmental adaptation mechanisms involved in the "gut-organ" axes. Results Significant differences in gut microbiota were found among different chicken populations sampled from across China, governed by variations in habitat species pools and species turnover. A more complex and stochastic-dominated gut microbiota with higher functional redundancy was observed in the Tibetan chicken population living in the plateau environment. Furthermore, Tibetan chickens also had more effective fatty acid degradation capacity, corresponding to their hypoxic environment. In contrast, chickens living in lowland breeding farms showed stronger immune system responses for defense against frequent health threats. These environmental adaptation strategies were found to be regulated by core gut microbes taxa in the phylum Firmicutes. Conclusions Our findings demonstrate the roles of breed and habitat in gut microbiota assembly of chickens, and clarifies the adaptation strategies of chickens to environmental changes via gut microbiota-driven "gut-organ" axes.