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Metagenomic Analysis of Silage
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Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation
Xuesong Xiang1, Yingying Li1, Junbin Ye2
1Key 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 Prevention, Beijing, China.
NPJ Biofilms and Microbiomes
|July 18, 2025
Summary
Traditional Chinese fermented foods harbor diverse microbes, but some pose risks. This study found potential pathogen and antibiotic resistance gene transfer from fermented soybean products to the human gut microbiome, highlighting food safety concerns.
Area of Science:
- Microbiology
- Food Science
- Genomics
Background:
- Fermented foods are integral to Chinese cuisine, known for gut health benefits.
- The microbial makeup of these foods is not well understood, posing potential health risks.
- Concerns exist regarding pathogens and antibiotic resistance genes (ARGs) in fermented products.
Purpose of the Study:
- To characterize the microbial and functional profiles of traditional Chinese fermented soybean products.
- To investigate the potential transfer of microbes and ARGs from these foods to the human gut.
- To assess the food safety implications of traditional fermentation practices.
Main Methods:
- Shotgun metagenomic sequencing was employed to analyze 93 samples of fermented soybean products.
- Microbial communities and functional genes were identified and compared across different food types.
- Comparative analysis with public Chinese gut microbiome data was performed.
Main Results:
- Distinct microbial and functional profiles were observed among the fermented food types.
- Antagonistic interactions were found between beneficial (Bacillales, Lactobacillales) and harmful (Enterobacterales) bacteria.
- Species and strains were shared between fermented foods and human gut microbiomes, with identification of pathogens like Klebsiella pneumoniae.
- Potential transfer of ARGs from food microbes to gut bacteria was indicated.
Conclusions:
- Certain traditional Chinese fermented soybean products may harbor clinically relevant pathogens and ARGs.
- There is evidence of microbial and genetic exchange between these foods and the human gut.
- Integrating microbial surveillance into fermentation processes is crucial for ensuring food safety while retaining health benefits.
