Core bacterial community of soy-daddawa: Insights from high-throughput DNA metabarcoding

Abstract

High-throughput sequence analysis of microbial communities in food matrices provides unprecedented insights into species richness and potential safety of foods. Here, the bacterial community of soy-daddawa, a fermented indigenous food condiment, was investigated for the first time using high-throughput DNA metabarcoding (16S rRNA gene). Analyses of 1 246 692 high-quality 16S rRNA gene sequences obtained from seven soy-daddawa samples/producers yielded 1520 operational taxonomic units (OTUs). Beta-diversity analysis of soy-daddawa bacterial communities suggested differences between samples, and in some cases, clustering according to geographical proximity of producers. Sixty-five OTUs (taxonomically assigned to 13 phylotypes) comprised the core (100% threshold) bacterial community of soy-daddawa and included Bacillus amyloliquefaciens, B. lichenformis, B. mojavensis, B. pumilus, B. subtilis, B. subtilis subsp. spizizenii, B. tequilensis, Exiguobacterium sp., Staphylococcus epidermidis and S. pseudintermedius. However, genera with known pathogenic species such as Atopostipes, Enterococcus, Granulicatella, Nosocomicoccus, Proteus, Pseudomonas and Vagoccoccus constituted at least 1% (relative abundance) in at least one sample. Insights gained from this study are useful for the development of a starter culture technology for the controlled fermentation of soy-daddawa. Also, the presence of potentially pathogenic species corroborates established global consensus on the microbiological risks associated with spontaneously fermented indigenous foods.