title: 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.
authors.affiliation: Unit of Environmental Sciences and Management, North-West University, Potchefstroom Campus, 2520, South Africa; Department of Microbiology, Federal University of Agriculture, PMB 2240 Abeokuta, Ogun State, Nigeria.
authors.forename: Obinna T
authors.initials: OT
authors.lastname: Ezeokoli
authors.affiliation: Unit of Environmental Sciences and Management, North-West University, Potchefstroom Campus, 2520, South Africa.
authors.forename: Arvind K
authors.initials: AK
authors.lastname: Gupta
authors.affiliation: Unit of Environmental Sciences and Management, North-West University, Potchefstroom Campus, 2520, South Africa.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Mienie
authors.affiliation: Department of Microbiology, Federal University of Agriculture, PMB 2240 Abeokuta, Ogun State, Nigeria. Electronic address: tospopoola@yahoo.com.
authors.forename: Temitope O S
authors.initials: TO
authors.lastname: Popoola
authors.affiliation: Unit of Environmental Sciences and Management, North-West University, Potchefstroom Campus, 2520, South Africa.
authors.forename: Cornelius C
authors.initials: CC
authors.lastname: Bezuidenhout
mesh_terms: D001419:Bacteria / Q000235:genetics*; D003212:Condiments / Q000382:microbiology*; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D058645:Denaturing Gradient Gel Electrophoresis; D005516:Food Microbiology; D005658:Fungi / Q000235:genetics*; D009549:Nigeria; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013025:Glycine max
chemical_list: D021903:DNA, Ribosomal Spacer; D012336:RNA, Ribosomal, 16S
keywords: Bacteria; Condiment; Fermentation; Fungi; Microbial community; PCR-DGGE; Soy-daddawa