A genomics-based investigation of acetic acid bacteria across a global fermented food metagenomics dataset

Developing a better understanding of the genomic and metabolic features of acetic acid bacteria (AABs) has the potential to facilitate an improvement of the taste or flavor of fermented foods. Here, we conducted a high-resolution analysis of AABs present in fermented foods based on the investigation of 337 high-quality metagenomic-assembled genomes (MAGs) recovered from 223 metagenomic samples. Firstly, by integrating these MAGs, we built a phylogenetic tree of high-quality MAGs using GTDB-Tk. We found that AABs MAGs from food-related samples and those from other environments are generally phylogenetically distinct, with the majority of those from fermented foods being assigned to a relatively small number of genera. Functional metagenomic analysis also revealed that the fermented food-associated AABs MAGs are associated with the production of carbohydrate-active enzymes, antibiotic resistance genes, and secondary metabolites. Through these investigations, we have gained substantial insights into the diversity, function, and roles of AABs in fermented food microbiomes.