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The gut microbiota significantly affect host nutrition, metabolism, and immunity. Hence, characterization of the gut microbial structure and function will improve our understanding of gut microbial resources and the mechanisms underlying host\u2013microbe interactions. Here, we investigated the gut microbiomes of seven pig breeds using metagenomics and 16S rRNA gene amplicon sequencing. We established an expanded gut microbial reference catalog comprising 17\u2009020\u2009160 genes and identified 4910 metagenome-assembled genomes. We also analyzed the gut resistome to provide an overview of the profiles of the antimicrobial resistance genes in pigs. By analyzing the relative abundances of microbes, we identified three core-predominant gut microbes (Phascolarctobacterium succinatutens, Prevotella copri, and Oscillibacter valericigenes) in pigs used in this study. Oral administration of the three core-predominant gut microbes significantly increased the organ indexes (including the heart, spleen, and thymus), but decreased the gastrointestinal lengths in germ-free mice. The three core microbes significantly enhanced intestinal epithelial barrier function and altered the intestinal mucosal morphology, as was evident from the increase in crypt depths in the duodenum and ileum. Furthermore, the three core microbes significantly affected several metabolic pathways (such as \u201csteroid hormone biosynthesis,\u201d \u201cprimary bile acid biosynthesis,\u201d \u201cphenylalanine, tyrosine and tryptophan biosynthesis,\u201d and \u201cphenylalanine metabolism\u201d) in germ-free mice. These findings provide a panoramic view of the pig gut microbiome and insights into the functional contributions of the core-predominant gut microbes to the host.<\/jats:p>","DOI":"10.1093\/ismejo\/wrad037","type":"journal-article","created":{"date-parts":[[2024,1,2]],"date-time":"2024-01-02T16:46:31Z","timestamp":1704213991000},"source":"Crossref","is-referenced-by-count":52,"title":["Characterizing core microbiota and regulatory functions of the pig gut microbiome"],"prefix":"10.1093","volume":"18","author":[{"given":"Jun","family":"Hu","sequence":"first","affiliation":[{"name":"National Key Laboratory of Agricultural Microbiology , Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong , Wuhan, Hubei 430070 , China"},{"name":"Agricultural University , Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, Huazhong , Wuhan, Hubei 430070 , China"},{"name":"The Cooperative Innovation Center for Sustainable Pig Production , Wuhan, Hubei 430070 , China"},{"name":"Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology , Wuhan, Hubei 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianwei","family":"Chen","sequence":"additional","affiliation":[{"name":"BGI Research , Qingdao, Shandong 266555 , China"},{"name":"Laboratory of Genomics and Molecular Biomedicine , Department of Biology, , Copenhagen 2100 , Denmark"},{"name":"University of Copenhagen , Department of Biology, , Copenhagen 2100 , Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Libao","family":"Ma","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Agricultural Microbiology , Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, , Wuhan, Hubei 430070 , China"},{"name":"Huazhong Agricultural University , Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, , Wuhan, Hubei 430070 , China"},{"name":"The Cooperative Innovation Center for Sustainable Pig Production , Wuhan, Hubei 430070 , China"},{"name":"Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology , Wuhan, Hubei 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiliang","family":"Hou","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Agricultural Microbiology , Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, , Wuhan, Hubei 430070 , China"},{"name":"Huazhong Agricultural University , Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, , Wuhan, Hubei 430070 , China"},{"name":"The Cooperative Innovation Center for Sustainable Pig Production , Wuhan, Hubei 430070 , China"},{"name":"Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology , Wuhan, Hubei 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Genetics , Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, , Guiyang, Guizhou 550025 , China"},{"name":"Guizhou University , Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, , Guiyang, Guizhou 550025 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangfeng","family":"Kong","sequence":"additional","affiliation":[{"name":"Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process , Institute of Subtropical Agriculture, , Changsha, Hunan 410125 , China"},{"name":"Chinese Academy of Sciences , Institute of Subtropical Agriculture, , Changsha, Hunan 410125 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingguo","family":"Huang","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Hunan Agriculture University , Changsha, Hunan 410128 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhonglin","family":"Tang","sequence":"additional","affiliation":[{"name":"Shenzhen Branch , Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, , Shenzhen 518124 , China"},{"name":"Chinese Academy of Agricultural Sciences , Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, , Shenzhen 518124 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Wei","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Agricultural Microbiology , Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, , Wuhan, Hubei 430070 , China"},{"name":"Huazhong Agricultural University , Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, , Wuhan, Hubei 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangru","family":"Wang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Agricultural Microbiology , Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, , Wuhan, Hubei 430070 , China"},{"name":"Huazhong Agricultural University , Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, , Wuhan, Hubei 430070 , China"},{"name":"The Cooperative Innovation Center for Sustainable Pig Production , Wuhan, Hubei 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianghua","family":"Yan","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Agricultural Microbiology , Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, , Wuhan, Hubei 430070 , China"},{"name":"Huazhong Agricultural University , Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, College of Veterinary Medicine, , Wuhan, Hubei 430070 , China"},{"name":"The Cooperative Innovation Center for Sustainable Pig Production , Wuhan, Hubei 430070 , China"},{"name":"Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology , Wuhan, Hubei 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,1,12]]},"reference":[{"key":"2024030413110352700_ref1","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1016\/j.tim.2017.05.004","article-title":"Gut microbiota dysbiosis in postweaning piglets: understanding the keys to health","volume":"25","author":"Gresse","year":"2017","journal-title":"Trends Microbiol"},{"key":"2024030413110352700_ref2","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/486453a","article-title":"Model pigs face messy 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