Whole-genome Metagenomic Sequencing Reveals Gut Microbiota Composition and Function Associated with Differential Growth Performance in Two Chicken Breeds

Growth performance, an important trait in the broiler industry, is defined by both the host genome and gut microbiota. At present, it is not known how gut microbiota contribute to the growth of Dahen broilers, a commercially important breed in China. In this study, we used metagenome sequencing to compare the taxonomic composition and functional implications of cecal microbiota in fast-growing Dahen broilers and slow-growing Tibetan chickens. A total of 2,207,811 unique genes were assembled in the non-redundant set, and 99% of them were taxonomically annotated as having a bacterial origin. The fast-growing group displayed a higher alpha diversity than the slow-growing group in terms of ACE, Chao1, and Good's coverage statistics. The two groups presented also significantly different (<i>P</i> < 0.05) relative abundances of the genera <i>Collinsella</i>, <i>Olsenella</i>, <i>Pyramidobacter</i>, <i>Basidiobolus</i>, and <i>Mieseafarmvirus</i>, along with that of eight species (e.g., <i>Olsenella timonensis</i> and <i>Victivallis sp. Marseille Q1083</i>). Although not statistically significant, we found a higher expression of several energy metabolism-related eggNOG terms in the fast-growing group. In summary, the present study identifies gut microbiota associated with growth performance in Dahen broilers and offers new tools for gut microbiome-related intervention in this breed.