Species Composition and Phylogenetic Diversity of Acetic Acid Bacteria Communities in Homemade Vinegars

Despite their significance, the diversity of acetic acid bacteria (AAB) in homemade vinegars remains understudied. This study aimed to explore the species-level diversity of AAB in homemade vinegars and to assess their community structure to better understand this microbial niche. To investigate the diversity of these bacteria, we employed recently established customized 16S-23S rDNA internal transcribed spacer (ITS) amplicon metagenomics to identify AAB at the species level. By applying Hill numbers, we calculated species richness, relative abundance, and dominance, providing a clearer understanding of the community structure of AAB in 11 homemade vinegars. Although species richness was relatively high, both relative abundance and dominance were considerably lower, suggesting a community structure dominated by a few highly abundant taxa, with most species being rare or low in abundance. The most dominant genera across most samples were Komagataeibacter and Acetobacter, both of which are known for their roles in oxidative fermentation. Several previously unreported, potentially novel species of AAB were identified, along with two potentially novel genera. This is one of the first studies to examine the diversity of AAB in homemade vinegars using a culture-independent amplicon metagenomic approach. Our findings suggest that the microbiota of homemade vinegars remains an underexplored niche and a source for novel species with biotechnological potential. The results provide valuable baseline data for future microbial studies and may help in the development of novel, customized starter cultures for the improvement and standardization of vinegar production.