PCR-denaturing gradient gel electrophoresis analysis of microbial community in soy-daddawa, a Nigerian fermented soybean (Glycine max (L.) Merr.) condiment.

Abstract Soy-daddawa , a fermented soybean ( Glycine max (L.) Merr.) condiment, plays a significant role in the culinary practice of West Africa. It is essential to understand the microbial community of soy-daddawa for a successful starter culture application. This study investigated the microbial community structure of soy-daddawa samples collected from Nigerian markets, by PCR-denaturing gradient gel electrophoresis (DGGE) targeting the V3–V5 region of the 16S rRNA gene of bacteria and internal transcribed spacer 2 (ITS2) region of fungi. Six bacterial and 16 fungal (nine yeasts and seven molds) operational taxonomic units (OTUs)/species were obtained at 97% sequence similarity. Taxonomic assignments revealed that bacterial OTUs belonged to the phyla Firmicutes and Actinobacteria , and included species from the genera Atopostipes , Bacillus , Brevibacterium and Nosocomiicoccus . Densitometric analysis of DGGE image/bands revealed that Bacillus spp. were the dominant OTU/species in terms of population numbers. Fungal OTUs belonged to the phyla Ascomycota and Zygomycota , and included species from the genera, Alternaria , Aspergillus , Candida , Cladosporium , Dokmaia , Issatchenkia , Kodamaea , Lecythophora , Phoma , Pichia , Rhizopus , Saccharomyces and Starmerella . The majority of fungal species have not been previously reported in soy-daddawa . Potential opportunistic human pathogens such as Atopostipes suicloacalis , Candida rugosa , Candida tropicalis , and Kodamaea ohmeri were detected. Variation in soy-daddawa microbial communities amongst samples and presence of potential opportunistic pathogens emphasises the need for starter culture employment and good handling practices in soy-daddawa processing.