Meta-analysis of microbiomes reveals metagenomic features of fermented vegetables

An insightful exploration of the fermented vegetable microbiome is the key to improving food quality and sustainability. Based on 57 fermented vegetable samples from China, Ireland, the UK, and Germany retrieved from public genome databases, we conducted a high-resolution meta-analysis of the fermented vegetable microbiomes. There were significant differences in the microbiota composition and functional pathway diversity of the tested samples, as reflected by the differences in their geographical origins. Metagenomic analysis also revealed the metagenomic features of carbohydrate-active enzymes and antibiotic resistance genes in the fermented vegetable metagenomes. Five putative new species were detected by recovering 221 metagenomeassembled genomes belonging to the genera Rubrobacteraceae, Bifidobacteriaceae, and Ruminococcaceae. Our results provide new ecological insights into the implications of fermented vegetable microbiota composition and functional potential and highlight the importance of high-resolution metagenomic analysis to further investigate the fermented food microbiome.

Automated summary

Through a high-resolution meta-analysis of 57 fermented vegetable samples from China, Ireland, the UK, and Germany, we found significant differences in the microbiota composition and functional pathway diversity of fermented vegetables that are correlated with their geographical origins. Our metagenomic analysis also revealed the characteristics of carbohydrate-active enzymes and antibiotic resistance genes in fermented vegetable metagenomes. This study provides new ecological insights and emphasizes the importance of high-resolution metagenomic analysis in studying the fermented food microbiome.