Metagenomics-based characterization of fecal microbiome and resistome of laying hens during the production cycle

Ying-Qian Gao¹Qing-Yu Hou¹Xin-Wen Hou¹Yong-Jie Wei¹Kai-Meng Shang¹He Ma¹Hong-Li Geng¹Rui Liu¹Li-Hua Yang^2*Hany M. Elsheikha^3*Hong-Bo Ni¹Yu-Feng Huang^1*

• ¹Qingdao Agricultural University, Qingdao, China
• ²Changchun Sci-Tech University, Shuangyang, China
• ³University of Nottingham School of Medicine, Nottingham, United Kingdom

The extensive use of antimicrobials in livestock has led to the emergence of antimicrobial resistance (AMR) in microbes, raising global concerns about its hazards. Antibiotic resistance genes (ARGs) and their mobile genetic elements (MGEs) are often identified from poultry faeces. However, there are limited studies on the microbial community characteristics and ARGs of laying hens at different laying stages. In this study, a total of 40 fecal samples were collected from five sampling points corresponding to the early laying stage (HE), three peak laying stages (HPI, HPII, HPIII), and the late laying stage (HL), with eight samples randomly collected at each point. Comprehensive metagenomic sequencing was performed on all samples to characterize the structure and functional profiles of the intestinal microbial community and to systematically analyze the diversity and distribution patterns of ARGs. Most of the ARGs in the intestinal tract were found in bacteria belonging to Pseudomonadota and Bacillota, with Escherichia coli serving as the primary carrier of antibiotic resistance genes. Furthermore, a significant correlation was observed between the co-abundance and co-occurrence of ARGs and MGEs, suggesting that MGEs are likely key drivers of ARGs dissemination. These findings provided novel insights into the prevalence of ARGs in laying hens across different stages and may inform strategies to mitigate the spread of ARGs.