Genetic Background Behind the Amino Acid Profiles of Fermented Soybeans Produced by Four Bacillus spp

Abstract

Strains of four Bacillus spp. were respectively inoculated into sterilized soybeans and the free amino acid profiles of the resulting cultures were analyzed to discern their metabolic traits. After 30 days of culture, B. licheniformis showed the highest production of serine, threonine, and glutamic acid; B. subtilis exhibited the highest production of alanine, asparagine, glycine, leucine, proline, tryptophan, and lysine. B. velezensis increased the γ-aminobutyric acid (GABA) concentration to >200% of that in the control samples. B. sonorensis produced a somewhat similar amino acid profile with B. licheniformis. Comparative genomic analysis of the four Bacillus strains and the genetic profiles of the produced free amino acids revealed that genes involved in glutamate and arginine metabolism were not common to the four strains. The genes gadA/B (encoding a glutamate decarboxylase), rocE (amino acid permease), and puuD (γ-glutamyl-γ-aminobutyrate hydrolase) determined GABA production, and their presence was species-specific. Taken together, B. licheniformis and B. velezensis were respectively shown to have high potential to increase concentrations of glutamic acid and GABA, while B. subtilis has the ability to increase essential amino acid concentrations in fermented soybean foods.

Keywords: Bacillus; Soybean fermentation; gadA/B; puuD; rocE; γ-aminobutyric acid.

Fig. 1

Growth (A) and pH changes (B) of soybean cultures inoculated with four Bacillus strains over 30 days of incubation.

Fig. 2. Principal component analysis loadings from four Bacillus spp.-inoculated soybean samples over 30 days of incubation for (A) amino acid concentrations and (B) factor scores.

Numbers indicate the incubation time of samples in days.

Fig. 3. Venn diagram showing the pan-genome of four Bacillus spp. strains.

Overlapping regions represent common coding sequences (CDSs) shared between the genomes. The numbers outside the overlapping regions indicate the numbers of CDSs in each genome without homologs in the other genomes.

Fig. 4

Identification of genes involved in the amino acid metabolism of four Bacillus spp. strains.

Fig. 5. Structures of genes surrounding the annotated gabT gene in four Bacillus genomes.

Abbreviations: gabR, HTH-type transcriptional regulatory protein-encoding gene; gabT, GABA aminotransferase-encoding gene; rocE, amino acid permease-encoding gene; gabD, succinate-semialdehyde dehydrogenase-encoding gene.