Soybean fermentation: Microbial ecology and starter culture technology

Figures & data

Figure 1. Soybean consumption constraints and possible ways for their reduction/elimination. Photos of soybeans seeds dehull seeds and dicotyledon structures are included. This figure was created using BioRender (https://biorender.com/).

Figure 2. Process flow diagram of soybeans. This figure was created using BioRender (https://biorender.com/).

Table 1. Comparison of microbial roles in spontaneously fermented soybean products.

Dominant microbial species found in fermented soy products	Fermentation types	Fermented soybean products	Main functions	References
Bacillus subtilis var. natto B. amyloliquefaciens, B. licheniformis B. pumilus B. velezensis	Alkaline fermentation	Natto Kinema Douchi	Produced polyglutamic acid, which was the major component of the viscous sticky mucilage that was found in Natto Produced distinct flavor compounds associated with pungent that gave Natto its characteristic aroma Exhibited amylolytic, proteolytic, and lipolytic activity that could break down carbohydrates, proteins, and lipids into smaller products	(Shin and Jeong 2015; Shrestha, Dahal, and Ndungutse 2013)
Mucor spp. Actinomucor spp.	Fungal fermentation	Sufu Tempeh	High protease production broke down proteins into smaller peptides and amino acids Formed a product with a soft cheese-like texture with a creamy consistency (Sufu)	(Wei, Regenstein, and Zhou 2021)
Aspergillus spp.	Fungal fermentation	Soya sauce Miso Sufu Tempeh	Produced enzymes such as cellulase, amylase, and proteases Produced glutaminase that converted glutamine to glutamic acid to provide a distinct umami flavor Produced 4-ethyl guaiacol (characteristic soy sauce aroma)	(Kusumoto et al. 2021; Yamashita 2021).
Rhizopus spp.	Fungal fermentation	Tempeh Sufu	Formed mycelia to fuze fermented soybeans together to form a ‘cake-like’ product Produced carbohydrate degradation enzymes, lipases, and proteases	(Handoyo and Morita 2006; Mulyowidarso 1991; Sarkar and Nout 2014).
Tetragenococcus halophilus	Third fermentation (Maturation)	Soy sauce Miso Sufu	Salt tolerant bacteria Produced lactic acid to reduce pH	(Allwood, Wakeling, and Bean 2021)
Zygosaccharomyces rouxiiin Millerozyma spp. Candida spp.	Third fermentation (Maturation)	Douchi Soy sauce Sufu Miso	Produced flavor compounds such as (3-octanol, 2-methoxy-phenol, 4-ethyl-phenol, and phenol) Produced esters that enhanced sweet and caramel-like aroma	Wang et al. 2022; Zhao et al. 2023)
Monascus purpureus	Third fermentation (Maturation)	Red Sufu	Produced red pigments that gave Sufu its characteristic reddish appearance	(Xie et al. 2018)

Table 2. Bacterial and yeast starter cultures diversity in soybean fermentation.

Starter cultures	Characteristics of the selected strains	Contribution to the fermentation process and soybeans quality	References
Bacillus subtilis	High resistance High enzymatic activities Anti-microbial	Desirable metabolites: butanone, 2-methylbutanoic acid, trimethyl pyrazines, 2-pentrylfuran, 3-hydroxybutanone, and dimethyl disulfide Increased phenolics Improved the digestibility, Removed the beany odor and indigestible oligosaccharides	(Leejeerajumnean et al. 2001; Liu, Song, and Luo 2018; Owens et al. 1997; Sarkar and Tamang 1995; Shrestha, Dahal, and Ndungutse 2013; Shrestha and Noomhorm 2001)
Bacillus polyfermenticus	High fibrinolytic High proteolytic High polyglutamate production	Low viscosity Functional food	(Mo et al. 2010)
Bacillus amyloliquefaciens	High proteolytic B- glucosidase	Accelerated the fermentation Increased phenolics Reduced the anti-nutritive	(Cho et al. 2003; Jiang et al. 2019; Wang, Zhang, et al. 2021; Yang et al. 2019)
Bacillus velezensis		Decreased allergenicity Improved digestibility Showed Antimicrobial effects	(Liu, Chen, et al. 2021)
Lactobacillus rhamnosus Tetragenococcus halophilus Lactiplantibacillus plantarum Levilactobacillus brevis Lactcaseibacillus paracasei Lactobacillus casei Liquorilactobacillus mali Bifidobacterium breve	Produce organic acids and antimicrobial metabolites to inhibit food contamination and foodborne pathogens Add desirable flavors Halophilic pH tolerance	Improved the product sensory quality Increased its antioxidant capacity Improved the product texture Increased the concentration of amino acids Reduced the concentration of biogenic amines Enhanced product stability, Desirable volatile compounds Encouraged yeasts growth	(Chen, Yanagida, and Hsu 2006; Holzapfel et al. 2006; Liu et al. 2012; Marazza et al. 2012; Nguyen et al. 2007; Ouoba et al. 2005; Sarkar and Nout 2014; Sarkar and Tamang 1994; Shimakawa et al. 2003; Sirilun et al. 2017; Yoon, Kim, and Hwang 2008)
Saccharomyces Klyveromyces Debaryomyces Hansenula Meyerozyma guilliermondii Rhodoturola Zygosaccharomyces	Organic acids tolerance Osmotolerance pH tolerance Production of various desirable metabolites Produce proteases, galactosidases, invertases, and inulinases	Increased protein contents Improved the antioxidant activities Reduced the crude fiber level	(Arneborg et al., 2000; Deak, 2007; Lee et al. 1997; Rashad et al. 2011; Sarkar and Tamang 1994; Song, Jeong, and Baik 2015; Sørensen et al. 2011)
Zygosaccharomyces	Grow at high salt content Produce desirable metabolites	Improved the final product sensory quality	(Kwon and Kim 2005)
Zygosaccharomyces rouxii M. guilliermondii	–	Produced desirable metabolites (furanone, and higher alcohols) Added sweet and caramel flavor notes	(Hayashida, Nishimura, and Slaughter 1997; Kim et al. 2011; Wah et al. 2013)
Kluyveromyces marxianus	–	Increased crude fat, soluble dietary fibers, and polysaccharides Reduced anti-nutritive factors Reduced beany odor	(Hu et al. 2019)
Lindnera saturnus	Metabolize aldehydes such as 2-heptenal and hexanal that are responsible for green beany flavor and bioconvert them into corresponding ester compounds ethyl hexanoate and ethyl heptanoate	Improved the bean quality Added fruity and sweet aroma	(Vong and Liu 2018)
Candida parapsilosis Geotrichum candidum	-	Created a low-quality final product with an undesirable rancid smell	(Sarkar and Tamang 1994)

Table 3. Filamentous fungi starter cultures diversity in soybean fermentation.

Filamentous fungi	Most characteristics of the selected strains	Contribution to the fermentation process and soybeans quality	References
Mucor racemosus Mucor Sufu Actinomucor elegans Actinomucor taiwanensis	Narrow temperature tolerance between 20-30^oC	Increased amino acids concentration Degraded the fiber content Masked the fishy smell Had smooth mouthfeel and sensory quality	(Cheng et al. 2009; Krishna 2005; Kronenberg and Hang 1984; Xu, Liu, and Zhou 2012)
Mucor flavus	Grow at low temperature (15^oC) Potential proteolytic enzyme activities	Increased amino acid levels in the final product	(Cheng et al. 2009)
Aspergillus oryzae Aspergillus sajae	Saccharification capabilities High proteolytic	Improved color aroma and sensory quality to the fermented beans Neither of them produced mycotoxins Produced various flavors and aroma compounds Produced high abundant glutamic acid (added umami taste)	(Kitamoto 2002; Ohata et al. 2007)
Rhizopus oligosporus Rhizopus oryzae	Growth at high temperatures makes it suitable for summer-season production High proteolytic and amylolytic activities Antimicrobial activities Desire volatiles producer	Improved the product regarding alkalinization, taste, and texture Increased the level of vitamins	(Baumann and Bisping 1995; Sparringa and Owens 1999)
Penicillium glabrum	α-ketoglutaric acid-derived amino acid synthesis	Modulated the nutrient profile compared to A. oryzae fermented beans	(Sun et al. 2019)

Figure 3. Starter culture selective criteria in soybean fermentation. This figure was created using BioRender (https://biorender.com/).

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