Micro-coevolution of host genetics with gut microbiome in three Chinese ethnic groups |
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| Affiliation: | 1. Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China;2. Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China;3. State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China;4. School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China;5. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China;6. Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China;7. Human Phenome Institute, Fudan University, Shanghai 201203, China;1. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China;2. School of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China;3. School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100101, China;1. High Altitude Medical Research Center of Tibet University/Center of Tibetan Studies (Everest Research Institute), Tibet University, 10 East Zangda Road, Lhasa, Tibet 850000, China;2. State Key Laboratory of Genetic Engineering, School of Life Sciences & Human Phenome Institute, Fudan University, Shanghai 200438, China;3. Institute for Six-sector Economy, Fudan University, Shanghai 200433, China;4. Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China;5. Tibet University-Fudan University Joint Laboratory for Biodiversity and Global Change, Tibet University, 10 East Zangda Road, Lhasa, Tibet 850000, China;1. Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, National Resource Center for Non-Human Primates, Kunming Primate Research Center, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Kunming, Yunnan 650201, China;2. Kunming College of Life Sciences, University of Chinese Academy Sciences, Kunming, Yunnan 650204, China;3. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China;4. Laboratory of Molecular Genetics of Aging & Tumor, Medical Faculty, Kunming University of Science and Technology, Kunming, Yunnan 650500, China;1. College of Life Sciences, Zhejiang University, Hangzhou 310058, China;2. Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China;3. Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China;4. Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China;5. Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China;6. Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou 510275, China;7. Taizhou Hospital, Wenzhou Medical University, Linhai 325035, China;8. CAS Key Laboratory for Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China |
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| Abstract: | Understanding the micro-coevolution of the human gut microbiome with host genetics is challenging but essential in both evolutionary and medical studies. To gain insight into the interactions between host genetic variation and the gut microbiome, we analyzed both the human genome and gut microbiome collected from a cohort of 190 students in the same boarding college and representing 3 ethnic groups, Uyghur, Kazakh, and Han Chinese. We found that differences in gut microbiome were greater between genetically distinct ethnic groups than those genetically closely related ones in taxonomic composition, functional composition, enterotype stratification, and microbiome genetic differentiation. We also observed considerable correlations between host genetic variants and the abundance of a subset of gut microbial species. Notably, interactions between gut microbiome species and host genetic variants might have coordinated effects on specific human phenotypes. Bacteroides ovatus, previously reported to modulate intestinal immunity, is significantly correlated with the host genetic variant rs12899811 (meta-P = 5.55 × 10−5), which regulates the VPS33B expression in the colon, acting as a tumor suppressor of colorectal cancer. These results advance our understanding of the micro-coevolution of the human gut microbiome and their interactive effects with host genetic variation on phenotypic diversity. |
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| Keywords: | Micro-coevolution Gut microbiome Host genetics Uyghur Kazakh Han Chinese |
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