Exploring the Microbiome of Fermented Soy Products: Implications for Gut Health in China

Background: Fermented foods have a long history in China, and they continue to be widely consumed today. Fermented foods have recently been reported as a pivotal approach to restoring gut microbial diversity and are recommended by the International Scientific Association for Probiotics and Prebiotics for inclusion in dietary guidelines. However, there are potential safety concerns associated with fermented foods, such as the transfer of antibiotic resistance genes to the human gut. This underscores the need for a deeper understanding of the microbial communities in fermented foods and additional data to facilitate health risk assessments. Results: In this study, we employed shotgun metagenomic analysis to investigate the microbiota of three commonly consumed fermented soy products in China and compared them with the gut microbiota of the Chinese population. Our findings revealed significant differences in both the microbial composition and functions among these three fermented soy products. Intriguingly, network analysis revealed an antagonistic interaction between beneficial species Bacillales and Lactobacillales, and potentially harmful species Enterobacterales. In examining the Chinese gut microbiota, we identified a high prevalence of potentially harmful bacteria from the Enterobacterales order, which were also found in significant amounts in fermented foods. Using genome-level and strain-level analyses, we hypothesize that fermented foods may serve as a source of harmful bacteria, such as Klebsiella pneumoniae and Klebsiella quasipneumoniae, for gut microbiota. Horizontal gene transfer analysis highlighted the potential transfer of numerous antibiotic resistance genes from fermented foods microbes to those in the human gut microbiome. Conclusions: While there is substantial evidence supporting the potential health benefits of consuming fermented foods, our research highlights important safety concerns. Notably, consuming fermented foods could increase exposure to pathogenic microorganisms and increase the risk of antibiotic resistance gene transmission. This accentuates the need for enhanced microbial monitoring and quality control measures for fermented foods.