The multi-kingdom microbiome catalog of the chicken gastrointestinal tract  

作　　者：Yanan Wang Mengqi Qu Yuhai Bi William J.Liu Sufang Ma Bo Wan Yongfei Hu Baoli Zhu Gaiping Zhang George F.Gao 

机构地区：[1]International Joint Research Center of National Animal Immunology,College of Veterinary Medicine,Henan Agricultural University,Zhengzhou 450046,China [2]CAS Key Laboratory of Pathogen Microbiology and Immunology,Institute of Microbiology,Chinese Academy of Sciences(CAS),Beijing 100101,China [3]Longhu Laboratory,Zhengzhou 450046,China [4]University of Chinese Academy of Sciences,Beijing 100049,China [5]NHC Key Laboratory of Biosafety,National Institute for Viral Disease Control and Prevention,Chinese Center for Disease Control and Prevention,Beijing 102206,China [6]State Key Laboratory of Animal Nutrition and Feeding,College of Animal Science and Technology,China Agricultural University,Beijing 100193,China

出　　处：《Biosafety and Health》2024年第2期101-115,共15页生物安全与健康（英文）

基　　金：supported in part by grants from the National Key Research and Development Program of China(2023YFC2307101,2020YFA0509202);the Young TopNotch Talents Foundation of Henan Agricultural University(30501278);the major Scientific and Technological Project of Henan Province(221100110600);the Major Program of the National Natural Science Foundation of China(81991534);CAS Southeast Asia Biodiversity Research Institute(151C53KYSB20210023);the Self-supporting Program of Guangzhou Laboratory(SRPG22-001);the National Science and Technology Infrastructure of China(National Pathogen Resource Center-NPRC-32);supported by the Youth Innovation Promotion Association of CAS(Y2021034)。

摘　　要：Chicken is an important food animal worldwide and plays an important role in human life by providing meat and eggs.Despite recent significant advances in gut microbiome studies,a comprehensive study of chicken gut bacterial,archaeal,and viral genomes remains unavailable.In this study,we constructed a chicken multi-kingdom microbiome catalog(CMKMC),including 18,201 bacterial,225 archaeal,and 33,411 viral genomes,and annotated over 6,076,006 protein-coding genes by integrating 135 chicken gut metagenomes and publicly available metagenome-assembled genomes(MAGs)from ten countries.We found that 812 and 240 MAGs in our dataset were putative novel species and genera,respectively,far beyond what was previously reported.The newly unclassified MAGs were predominant in Phyla Firmicutes_A(n=263),followed by Firmicutes(n=126),Bacteroidota(n=121),and Proteobacteria(n=87).Most of the classified species-level viral oper-ational taxonomic units belong to Caudovirales.Approximately,63.24%of chicken gut viromes are predicted to infect two or more hosts,including complete circular viruses.Moreover,we found that diverse auxiliary metabolic genes and antibiotic resistance genes were carried by viruses.Together,our CMKMC provides the largest integrated MAGs and viral genomes from the chicken gut to date,functional insights into the chicken gastrointestinal tract microbiota,and paves the way for microbial interventions for better chicken health and productivity.

关 键 词：CHICKEN MICROBIOME Metagenome assembled genomes Archaeome Virome Antibiotic resistance gene 

分 类 号：Q93[生物学—微生物学]