Temporal variability in the diversity, function and resistome landscapes in the gut microbiome of broilers

作者：Jinxin Meng, Ming‐Han Li, Xiangyu Wang, Shenghui Li, Yue Zhang, Hong‐Bo Ni, He Ma, Rui Liu, Jin-Chu Yan, Xiaoman Li, Yu-Zhe Sun, Xing Yang, Xiao‐Xuan Zhang · 发表于：Ecotoxicology and Environmental Safety · 年份：2025 · DOI：10.1016/j.ecoenv.2025.117976 · 被引用次数：18 · 研究领域：Animal Nutrition and Physiology、Gut microbiota and health、Agriculture, Soil, Plant Science

Understanding the dynamic and stability of gut microbiota over the course of production cycle of broiler chicken can help identify microbial features that associate with better health and productivity. In the present study, we profile the changes in the composition and stability of gut microbiota of commercially raised broilers at nine distinct time points using shotgun metagenomics and culturomics approaches. We demonstrate, within the first week post-hatching, a rapid decline in relative abundance of 122 pioneer microbial species including Bacteroides fragilis , Lachnospira eligens and Ruminococcus gnavus , accompanied by a substantial decrease in both microbial richness and diversity. This was followed by a gradual increase and stabilization in the microbial diversity and population structure that persisted until the broilers reached the marketing age. Throughout the production cycle, key bacterial families such as Lachnospiraceae, Bacteroidaceae, and Ruminococcaceae were identified. However, significant shifts at the lower taxonomic levels occurred at different production stages, influencing the functional capacities and resistance profiles of the microbiota. During the rapid growth phase, enzymes crucial to vitamin and amino acid metabolism dominated, whereas enzymes associated with carbohydrate and energy metabolism were notably more abundant during the fattening stage. Many predicted antibiotic resistance genes were detected in association with typical commensal bacter...