Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigs
Abstract Compared with leaner breeds, local Chinese pig breeds have distinct intestinal microbial, as determined by metagenomic techniques, and the interactions between oral microorganisms and their hosts are also gradually being clarified. However, the high host genome content means that few metage...
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Nature Portfolio
2025-01-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04413-1 |
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| author | Hong Hu Ying Huang Fuyan Yang Liangru Ma Junjie Zhang Xu Deng Nan Ma Kunping Wang Ye Tao Qin Lin Yanfei Li Xi Bai Hongbin Pan |
| author_facet | Hong Hu Ying Huang Fuyan Yang Liangru Ma Junjie Zhang Xu Deng Nan Ma Kunping Wang Ye Tao Qin Lin Yanfei Li Xi Bai Hongbin Pan |
| author_sort | Hong Hu |
| collection | DOAJ |
| description | Abstract Compared with leaner breeds, local Chinese pig breeds have distinct intestinal microbial, as determined by metagenomic techniques, and the interactions between oral microorganisms and their hosts are also gradually being clarified. However, the high host genome content means that few metagenome-based oral microbiomes have been reported. Here, we combined dilution-based metagenomic sequencing and binning approaches to extract the microbial genomes from the oral microbiomes of Tibetan and Duroc pigs. The host contamination rates were reduced to 13.64%, a quarter of the normal metagenomic level (65.25% on average). Medium–high-quality metagenome-assembled genomes (MAGs; n = 3,448) spanning nine phyla were retrieved and 70.79% were novel species. Of the nonredundant MAGs, only 13.37% were shared, revealing the strong disparities between Tibetan and Duroc pigs. The oral microbial diversity of the Duroc pig was greater than that of the Tibetan pig. We present the first large-scale dilute-based metagenomic data on the pig oral microbiome, which should facilitate further investigation of the functions of oral microorganisms in pigs. |
| format | Article |
| id | doaj-art-b384800d6904403488f7b1e586a9627a |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
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| series | Scientific Data |
| spelling | doaj-art-b384800d6904403488f7b1e586a9627a2025-01-26T12:14:28ZengNature PortfolioScientific Data2052-44632025-01-011211710.1038/s41597-025-04413-1Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigsHong Hu0Ying Huang1Fuyan Yang2Liangru Ma3Junjie Zhang4Xu Deng5Nan Ma6Kunping Wang7Ye Tao8Qin Lin9Yanfei Li10Xi Bai11Hongbin Pan12Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural UniversityYunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural UniversityYunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural UniversityYunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural UniversityYunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural UniversityYunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural UniversityYunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural UniversityCollege of Animal Science, Anhui Science and Technology UniversityShanghai BIOZERON Biotechnology Company LtdShanghai BIOZERON Biotechnology Company LtdShanghai BIOZERON Biotechnology Company LtdCollege of Animal Science, Anhui Science and Technology UniversityYunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural UniversityAbstract Compared with leaner breeds, local Chinese pig breeds have distinct intestinal microbial, as determined by metagenomic techniques, and the interactions between oral microorganisms and their hosts are also gradually being clarified. However, the high host genome content means that few metagenome-based oral microbiomes have been reported. Here, we combined dilution-based metagenomic sequencing and binning approaches to extract the microbial genomes from the oral microbiomes of Tibetan and Duroc pigs. The host contamination rates were reduced to 13.64%, a quarter of the normal metagenomic level (65.25% on average). Medium–high-quality metagenome-assembled genomes (MAGs; n = 3,448) spanning nine phyla were retrieved and 70.79% were novel species. Of the nonredundant MAGs, only 13.37% were shared, revealing the strong disparities between Tibetan and Duroc pigs. The oral microbial diversity of the Duroc pig was greater than that of the Tibetan pig. We present the first large-scale dilute-based metagenomic data on the pig oral microbiome, which should facilitate further investigation of the functions of oral microorganisms in pigs.https://doi.org/10.1038/s41597-025-04413-1 |
| spellingShingle | Hong Hu Ying Huang Fuyan Yang Liangru Ma Junjie Zhang Xu Deng Nan Ma Kunping Wang Ye Tao Qin Lin Yanfei Li Xi Bai Hongbin Pan Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigs Scientific Data |
| title | Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigs |
| title_full | Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigs |
| title_fullStr | Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigs |
| title_full_unstemmed | Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigs |
| title_short | Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigs |
| title_sort | metagenome assembled microbial genomes n 3 448 of the oral microbiomes of tibetan and duroc pigs |
| url | https://doi.org/10.1038/s41597-025-04413-1 |
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