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<p>Traditionally prepared fermented food products are the results of spontaneous fermentation and exhibit variable microbial diversities. Although the recent transition to plant-based diets is rising, the functional nutrition and probiotic properties of plant based fermented foods are much less explored. We performed a comparative metagenomic analysis of plant based fermented food across the world to explore the microbial diversity in terms of probiotics, nutritionally beneficial, and food safety aspects. The whole shotgun metagenomic sequencing of 12 fermented food samples and starter cultures from Himachal Pradesh, India were sequenced and 16S rRNA gene was extracted using in silico method. This data was analysed together with the 16S rRNA metagenomic datasets of 688 publicly available datasets from 23 other countries. A dominance of various microbial taxa associated with Lactic Acid Bacteria group including <i>Lactobacillus</i>,<i> Weissella</i>,<i> Lactiplantibacillus</i>, etc., largely associated with functions like fermentation and chemoheterotrophy, was observed in the plant based fermented foods worldwide. The presence of pathogenic functionalities towards humans was also observed, albeit in minor abundance, indicating towards the limitation of uncontrolled fermentation and risks involved in terms of food safety. Diversity analysis demonstrated a statistically significant difference in microbial diversity across countries, different types of substrates used, differences in fermentation techniques including the use of starter cultures as well spontaneous fermentation and the final products formed. Further, an exploration of the V3-V4 region to explore the microbial diversity is found to be most informative to explore the microbial diversity of fermented food products.</p>

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Comparative analysis using 16S rRNA metagenomics to explore the microbial diversity of plant based fermented foods

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年2月28日

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  • Harshita Sharma,
  • Rashmi Ira,
  • Diksha Sood,
  • Rajneesh Kumar,
  • Sarita Devi,
  • Tulika Prakash

摘要

Traditionally prepared fermented food products are the results of spontaneous fermentation and exhibit variable microbial diversities. Although the recent transition to plant-based diets is rising, the functional nutrition and probiotic properties of plant based fermented foods are much less explored. We performed a comparative metagenomic analysis of plant based fermented food across the world to explore the microbial diversity in terms of probiotics, nutritionally beneficial, and food safety aspects. The whole shotgun metagenomic sequencing of 12 fermented food samples and starter cultures from Himachal Pradesh, India were sequenced and 16S rRNA gene was extracted using in silico method. This data was analysed together with the 16S rRNA metagenomic datasets of 688 publicly available datasets from 23 other countries. A dominance of various microbial taxa associated with Lactic Acid Bacteria group including Lactobacillus, Weissella, Lactiplantibacillus, etc., largely associated with functions like fermentation and chemoheterotrophy, was observed in the plant based fermented foods worldwide. The presence of pathogenic functionalities towards humans was also observed, albeit in minor abundance, indicating towards the limitation of uncontrolled fermentation and risks involved in terms of food safety. Diversity analysis demonstrated a statistically significant difference in microbial diversity across countries, different types of substrates used, differences in fermentation techniques including the use of starter cultures as well spontaneous fermentation and the final products formed. Further, an exploration of the V3-V4 region to explore the microbial diversity is found to be most informative to explore the microbial diversity of fermented food products.