Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition
Lingyan Ma,
Wentao Lyu,
Tao Zeng,
Wen Wang,
Qu Chen,
Jiangchao Zhao,
Guolong Zhang,
Lizhi Lu,
Hua Yang,
Yingping Xiao
Affiliations
Lingyan Ma
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Agro‐product Safety and Nutrition Zhejiang Academy of Agricultural Sciences Hangzhou China
Wentao Lyu
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Agro‐product Safety and Nutrition Zhejiang Academy of Agricultural Sciences Hangzhou China
Tao Zeng
Institute of Animal Husbandry and Veterinary Medicine Zhejiang Academy of Agricultural Sciences Hangzhou China
Wen Wang
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Agro‐product Safety and Nutrition Zhejiang Academy of Agricultural Sciences Hangzhou China
Qu Chen
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Agro‐product Safety and Nutrition Zhejiang Academy of Agricultural Sciences Hangzhou China
Jiangchao Zhao
Department of Animal Science, Division of Agriculture University of Arkansas Fayetteville Arkansas USA
Guolong Zhang
Department of Animal and Food Sciences Oklahoma State University Stillwater Oklahoma USA
Lizhi Lu
Institute of Animal Husbandry and Veterinary Medicine Zhejiang Academy of Agricultural Sciences Hangzhou China
Hua Yang
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Agro‐product Safety and Nutrition Zhejiang Academy of Agricultural Sciences Hangzhou China
Yingping Xiao
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Agro‐product Safety and Nutrition Zhejiang Academy of Agricultural Sciences Hangzhou China
Abstract The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play an important role in duck health and production. Here, we constructed the first relatively comprehensive duck gut microbial gene catalog (24 million genes) and 4437 metagenome‐assembled genomes using 375 GIT metagenomic samples from four different duck breeds across five intestinal segments under two distinct rearing conditions. We further characterized the intestinal region‐specific microbial taxonomy and their assigned functions, as well as the temporal development and maturation of the duck gut microbiome. Our metagenomic analysis revealed the similarity within the microbiota of the foregut and hindgut compartments, but distinctive taxonomic and functional differences between distinct intestinal segments. In addition, we found a significant shift in the microbiota composition of newly hatched ducks (3 days), followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days), indicating that the intestinal microbiota develops into a relatively mature and stable community as the host duck matures. Comparing the impact of different rearing conditions (with and without water) on duck cecal microbiota communities and functions, we found that the bacterial capacity for lipopolysaccharide biosynthesis was significantly increased in ducks that had free access to water, leading to the accumulation of pathogenic bacteria and antibiotic‐resistance genes. Taken together, our findings expand the understanding of the microbiome signatures linked to intestinal regional, temporal development, and rearing conditions in ducks, which highlight the significant impact of microbiota on poultry health and production.
