Metagenomic Analysis Reveals Linkages Between Caecal Microbiota and Feed Efficiency in Xiayan Chicken

Abstract The caecal microbiota plays a critical role in energy harvest and nutrient digestion, influencing intestinal health, and the performance of chickens. Feed efficiency (FE) is essential for improving economic efficiency and saving social resources in chicken production and may be affected by the caecal microbiota. Therefore, to investigate the composition and functional capacity of cecum microbes related to FE in Xiayan chicken, an indigenous breed in Guangxi province, metagenome sequencing was performed on chicken caecal contents. 173 males and 167 females chicken were divided high and low feed efficiency according to residual feed intake (RFI), respectively. The caecal microbial genome was extracted and sequenced. The results showed that the genera Bacteroides, Prevotella, and Alistipes were the three most abundant in each caecal microbiome. LEfSe analysis revealed six potential biomarkers in males and 14 in females. Notably, the relative abundance of Lactobacillus in the high FE group was higher than the low FE group both in the male and female chickens, and the species Limosilactobacillus oris has a higher score in the high FE group of male chickens. In contrast, some potentially pathogenic microorganisms such as Campylobacter avium in females and Helicobacter pullorum in males were enriched in the low FE group. Predictive functional analysis showed that the high FE group in male chickens had a greater ability of xenobiotics biodegradation and metabolism and signaling molecules and interaction. Additionally, host sex was found to exert effects on caecal microbial composition and function associated with FE. These results increased our understanding of caecal microbial composition and identified many potential biomarkers related to FE, which may be used to improve the FE of the chickens.