Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation
Abstract Fermented foods are a longstanding part of the Chinese diet and have been recognized for promoting gut microbial diversity. However, their microbial composition remains poorly defined, raising concerns about potential exposure to pathogens and antibiotic resistance genes (ARGs). Using shotg...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-07-01
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| Series: | npj Biofilms and Microbiomes |
| Online Access: | https://doi.org/10.1038/s41522-025-00768-w |
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| author | Xuesong Xiang Yingying Li Junbin Ye Baolong Li Guozhong He Mingyu Zhu Jiawen Zhang Bike Zhang Ming Miao Yuexin Yang |
| author_facet | Xuesong Xiang Yingying Li Junbin Ye Baolong Li Guozhong He Mingyu Zhu Jiawen Zhang Bike Zhang Ming Miao Yuexin Yang |
| author_sort | Xuesong Xiang |
| collection | DOAJ |
| description | Abstract Fermented foods are a longstanding part of the Chinese diet and have been recognized for promoting gut microbial diversity. However, their microbial composition remains poorly defined, raising concerns about potential exposure to pathogens and antibiotic resistance genes (ARGs). Using shotgun metagenomics, we examined microbiota of 93 representative samples spanning three major categories of traditional Chinese fermented soybean products. We identified distinct microbial and functional profiles across food types, with antagonism between beneficial taxa (Bacillales and Lactobacillales) and harmful Enterobacterales. Comparative analysis with public Chinese gut microbiomes revealed species- and strain-sharing between fermented foods and human gut microbiota, identifying certain products as sources of clinically relevant pathogens, including Klebsiella pneumoniae and Klebsiella quasipneumoniae. Horizontal gene transfer analysis highlighted potential transfer of ARGs (e.g., efflux pump genes) from food microbes to gut microbiota. Our findings underscore the need to integrate microbial surveillance into traditional fermentation to balance health benefits with food safety. |
| format | Article |
| id | doaj-art-e84653ce47d7429887e6a39f44da34e7 |
| institution | Kabale University |
| issn | 2055-5008 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Biofilms and Microbiomes |
| spelling | doaj-art-e84653ce47d7429887e6a39f44da34e72025-08-20T03:42:40ZengNature Portfolionpj Biofilms and Microbiomes2055-50082025-07-0111111410.1038/s41522-025-00768-wChinese soy-based microbiome and associated microbial risks: a metagenomic investigationXuesong Xiang0Yingying Li1Junbin Ye2Baolong Li3Guozhong He4Mingyu Zhu5Jiawen Zhang6Bike Zhang7Ming Miao8Yuexin Yang9Key Laboratory of Public Nutrition and Health, National Health Commission of the People’s Republic of China, National Institute for Nutrition and Health, Chinese Center for Disease Control and PreventionKey Laboratory of Public Nutrition and Health, National Health Commission of the People’s Republic of China, National Institute for Nutrition and Health, Chinese Center for Disease Control and PreventionBeijing WeGenome Paradigm Co. LtdChinese PLA Center for Disease Control and PreventionKunming Medical UniversityKey Laboratory of Public Nutrition and Health, National Health Commission of the People’s Republic of China, National Institute for Nutrition and Health, Chinese Center for Disease Control and PreventionKey Laboratory of Public Nutrition and Health, National Health Commission of the People’s Republic of China, National Institute for Nutrition and Health, Chinese Center for Disease Control and PreventionNational Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and PreventionState Key Laboratory of Food Science & Resources, Jiangnan UniversityKey Laboratory of Public Nutrition and Health, National Health Commission of the People’s Republic of China, National Institute for Nutrition and Health, Chinese Center for Disease Control and PreventionAbstract Fermented foods are a longstanding part of the Chinese diet and have been recognized for promoting gut microbial diversity. However, their microbial composition remains poorly defined, raising concerns about potential exposure to pathogens and antibiotic resistance genes (ARGs). Using shotgun metagenomics, we examined microbiota of 93 representative samples spanning three major categories of traditional Chinese fermented soybean products. We identified distinct microbial and functional profiles across food types, with antagonism between beneficial taxa (Bacillales and Lactobacillales) and harmful Enterobacterales. Comparative analysis with public Chinese gut microbiomes revealed species- and strain-sharing between fermented foods and human gut microbiota, identifying certain products as sources of clinically relevant pathogens, including Klebsiella pneumoniae and Klebsiella quasipneumoniae. Horizontal gene transfer analysis highlighted potential transfer of ARGs (e.g., efflux pump genes) from food microbes to gut microbiota. Our findings underscore the need to integrate microbial surveillance into traditional fermentation to balance health benefits with food safety.https://doi.org/10.1038/s41522-025-00768-w |
| spellingShingle | Xuesong Xiang Yingying Li Junbin Ye Baolong Li Guozhong He Mingyu Zhu Jiawen Zhang Bike Zhang Ming Miao Yuexin Yang Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation npj Biofilms and Microbiomes |
| title | Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation |
| title_full | Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation |
| title_fullStr | Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation |
| title_full_unstemmed | Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation |
| title_short | Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation |
| title_sort | chinese soy based microbiome and associated microbial risks a metagenomic investigation |
| url | https://doi.org/10.1038/s41522-025-00768-w |
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