Comprehensive genomic insights into food-derived lactic acid bacteria reveal key roles in human health

Lactic acid bacteria (LAB) are indispensable microorganisms in fermented foods and have played a crucial role in human civilization's dietary development. They not only impart unique flavors and textures to fermented foods like yogurt and cheese but also significantly extend their shelf life. Furthermore, LAB are vital for human health, offering benefits such as promoting gut health and enhancing immunity. With the growing emphasis on healthy diets, the probiotic properties of LAB are increasingly recognized. However, due to their vast diversity and functional heterogeneity, there has been a lack of comprehensive datasets to systematically explore the diversity and metabolic potential of LAB.

To address this scientific gap, Professor Heping Zhang’s team conducted a global-scale collection of LAB from fermented foods and performed extensive genomic research. The result is a high-quality genomic database that spans a wide range of LAB species, serving as a critical resource for understanding LAB functionality and promoting their applications in food and health science.

The research team collected 6,202 samples of fermented foods from 85 countries, isolating 47,573 strains of LAB. Through high-throughput sequencing, they constructed a genomic database comprising 19,699 genomes, covering 5 families, 30 genera, and 143 species. This database significantly expands the available genomic resources for food-derived LAB. Genomic analyses revealed that LAB exhibits remarkable diversity and adaptability in key metabolic functions, such as carbohydrate metabolism and vitamin synthesis, highlighting their potential for food fermentation and functional development.

In addition to exploring genomic diversity, the study integrated data from 54 human gut microbiome disease cohorts (9,872 samples) to systematically compare LAB distribution in health and disease. The results revealed significant differences in LAB diversity between healthy and diseased states. For instance, individuals with gastrointestinal disorders showed a marked reduction in LAB diversity, while healthy individuals exhibited richer LAB communities. Based on these findings, the team developed a machine-learning model using random forest algorithms that can effectively distinguish between healthy and diseased states based on LAB characteristics. The study further identified 27 LAB species significantly enriched in healthy individuals, offering valuable clues for the development of functional foods and probiotic products.

This study systematically uncovers the diversity and metabolic potential of food-derived LAB, elucidating their critical roles in carbohydrate metabolism, vitamin synthesis, and gut health. The findings provide essential scientific evidence for the development of health-promoting foods and functional probiotics, paving the way for new strategies in gut microbiome intervention and precision nutrition. Future research will focus on the functional mechanisms of LAB-derived metabolites, further enhancing their applications in food, medicine, and nutrition science.

See the article:

A Genomic Compendium of Cultivated Food-Derived Lactic Acid Bacteria Unveils Their Contributions to Human Health

https://doi.org/10.1016/j.scib.2024.12.002