Whole-Genome Sequencing and Comparative Genome Analysis of Bacillus subtilis Strains Isolated from Non-Salted Fermented Soybean Foods.
Bacillus subtilis is the main component in the fermentation of soybeans. To investigate the genetics of the soybean-fermenting B. subtilis strains and its relationship with the productivity of extracellular poly-γ-glutamic acid (γPGA), we sequenced the whole genome of eight B. subtilis stains isolated from non-salted fermented soybean foods in Southeast Asia. Assembled nucleotide sequences were compared with those of a natto (fermented soybean food) starter strain B. subtilis BEST195 and the laboratory standard strain B. subtilis 168 that is incapable of γPGA production. Detected variants were investigated in terms of insertion sequences, biotin synthesis, production of subtilisin NAT, and regulatory genes for γPGA synthesis, which were related to fermentation process. Comparing genome sequences, we found that the strains that produce γPGA have a deletion in a protein that constitutes the flagellar basal body, and this deletion was not found in the non-producing strains. We further identified diversity in variants of the bio operon, which is responsible for the biotin auxotrophism of the natto starter strains. Phylogenetic analysis using multilocus sequencing typing revealed that the B. subtilis strains isolated from the non-salted fermented soybeans were not clustered together, while the natto-fermenting strains were tightly clustered; this analysis also suggested that the strain isolated from "Tua Nao" of Thailand traces a different evolutionary process from other strains.
Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
Mayumi
M
Kamada
Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
Sumitaka
S
Hase
Department of Biological Sciences, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
Kazushi
K
Fujii
Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
Masato
M
Miyake
Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
Kengo
K
Sato
Division of Applied Microbiology, National Food Research Institute, 2-1-12 12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan.
Keitarou
K
Kimura
Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
Yasubumi
Y
Sakakibara
D001412:Bacillus subtilis / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D005516:Food Microbiology; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D011099:Polyglutamic Acid / Q000031:analogs & derivatives* / Q000235:genetics / Q000378:metabolism; D045730:Soy Foods / Q000382:microbiology; D013025:Glycine max / Q000382:microbiology*; D013381:Subtilisins / Q000235:genetics; D013785:Thailand
D004251:DNA Transposable Elements; C511775:poly(gamma-glutamic acid); D011099:Polyglutamic Acid; D013381:Subtilisins; C053771:nattokinase