A genomics-powered review of diversity, function, and roles of acetic acid bacteria in fermented food

Acetic acid bacteria (AAB) have been widely studied for years due to their important role in the production of fermented foods. Understanding the genomic and metabolic features of AAB are critical in improving the taste, flavor, or mouthfeel of those foods. Here, we conducted a high-resolution meta-analysis of AAB in fermented foods based on 337 high quality metagenomic-assembled genomes (MAG) recovered from 223 metagenomic samples in order to better understand the genomes, geography, and predicted functions of the Acetobacteraceae. Firstly, by using MAGs from this study and the NCBI database, a phylogenetic tree of 609 high quality MAGs (337 out of 607 MAGs are from this study) was built by using GTDB-Tk. We found AAB MAGs are generally phylogenetically distinct between environmental and food-related samples, and the AAB community in fermented food is relatively concentrated, most of which are Acetobacter, Gluconobacter, Komagataeibacter, etc., but the genera of AAB in the environment sample are more diverse. Besides, to analyze the metabolic potential of AAB in fermented food, we annotated the genes with a variety database and reconstructed the metabolic functional traits. Results showed that the metabolic capabilities of AAB from different fermented foods differed with respect to some categories, such as carbohydrate and amino acid metabolism. Overall, our results provide new and substantial insights into the diversity, function, and roles of AAB in fermented food microbiome.