Whole-genome analysis of Bacillus subtilis G8 isolated from natto
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Abstract. Dikson, Victor H, Jong D, Sanjaya A, Samantha A, Jo J, Pinontoan R. 2022. Whole-genome analysis of Bacillus subtilis G8 isolated from natto. Biodiversitas 23: 1293-1300. Bacillus subtilis-fermented soy-based food is associated with multiple health benefits. Various bacterial strains have been isolated from it, includingB. subtilisG8, recent isolation from Japanese natto commercially available in Indonesia. Both 16S rRNA gene sequencing and fibrinolytic activity characterization have been performed and published in prior studies. After comparison to the genome of a natto-isolated reference strain (i.e., B. subtilisBEST195), the B. subtilis G8 genome showed a similar guanine-cytosine (GC) content, predicted number of coding sequences (CDS) and predicted number of tRNA genes, but had a shorter sequence length and fewer predicted rRNA genes. Further analysis using multiple genome alignment with Mauve, average nucleotide identity (ANI) matrix calculation, and phylogenetic inference indicated that B. subtilis G8 was more related to natto-derived B. subtilis than to cheonggukjang-derived B. subtilis and B. subtilis 168. Finally, sequence analyses of a gene encoding nattokinase as well as two genes regulating poly-gamma-glutamic acid (?-PGA) production in B. subtilis G8, B. subtilis BEST195 and B. subtilis 168 clearly indicated that B. subtilis G8 is able to produce nattokinase and ?-PGA, which both contribute to natto’s fermentation process. Therefore, it is proposed that B. subtilis G8 should be reclassified as B. subtilis subsp. natto G8 to reflect that it is a natto-derived B. subtilis strain.
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References
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403-410. DOI:10.1016/S0022-2836(05)80360-2
Auch AF, Henz SR, Holland BR, Göker M. 2006. Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences. BMC Bioinform 7:350. DOI:10.1186/1471-2105-7-350
Bang M-S, Jeong H-W, Lee Y, Lee SJ, Lee S-C, Shin J-I, Oh C-H. 2018. Complete genome sequence of Bacillus subtilis strain DKU_NT_02, isolated from traditional Korean food using soybean (chung-gook-jang) for high-quality poly-?-glutamic acid activity. Genome Announc 6:25. DOI:10.1128/genomeA.00525-18
Carver T, Berriman M, Tivey A, Patel C, Böhme U, Barrell BG, Parkhill J, Rajandream M-A. 2008. Artemis and ACT: Viewing, annotating and comparing sequences stored in a relational database. Bioinform 24:2672-2676. DOI:10.1093/bioinformatics/btn529
Chan EWC, Wong SK, Kezuka M, Oshiro N, Chan HT. 2021. Natto and miso: An overview on their preparation, bioactive components and health-promoting effects. Food Res 5:446-452. DOI:10.26656/fr.2017.5(3).587
Chen H, McGowan EM, Ren N, Lal S, Nassif N, Shad-Kaneez F, Qu X, Lin Y. 2018. Nattokinase: A promising alternative in prevention and treatment of cardiovascular diseases. Biomark Insights 13:1-13. DOI:10.1177/1177271918785130
Darling ACE, Mau B, Blattner FR, Perna NT. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14:1394-1403. DOI:10.1101/gr.2289704
Darling AE, Mau B, Perna NT. 2010. progressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5:e11147. DOI:10.1371/journal.pone.0011147
Edgar RC. 2004. MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinform 5:113. DOI:10.1186/1471-2105-5-113
Elshaghabee FMF, Rokana N, Gulhane RD, Sharma C, Panwar H, 2017. Bacillus as potential probiotics: status, concerns, and future perspectives. Front Microbiol 8:1490. DOI:10.3389/fmicb.2017.01490
Galata V, Fehlmann T, Backes C, Keller A. 2019. PLSDB: A resource of complete bacterial plasmids. Nucleic Acids Res 47:D195-D202. DOI:10.1093/nar/gky1050
García-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Götz S, Tarazona S, Dopazo J, Meyer TF, Conesa A. 2012. Qualimap: Evaluating next-generation sequencing alignment data. Bioinform 28:2678-2679. DOI:10.1093/bioinformatics/bts503
Heo J, Kim J-S, Hong S-B, Park B-Y, Kim S-J, Kwon S-W. 2019. Genetic marker gene recQ differentiating Bacillus subtilis and the closely related Bacillus species. FEMS Microbiol Lett 366:1-10. DOI:10.1093/femsle/fnz172
Hsueh Y-H, Huang K-Y, Kunene SC, Lee T-Y. 2017. Poly-?-glutamic acid synthesis, gene regulation, phylogenetic relationships, and role in fermentation. Int J Mol Sci 18:2644. DOI:10.3390/ijms18122644
Joshi NA, Fass JN. 2011. Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files. GitHub. https://github.com/najoshi/sickle
Kada S, Ishikawa A, Ohshima Y, Yoshida K. 2013. Alkaline serine protease AprE plays an essential role in poly-?-glutamate production during natto fermentation. Biosci Biotechnol Biochem 77:802-809. DOI:10.1271/bbb.120965
Kamada M, Hase S, Fujii K, Miyake M, Sato K, Kimura K, Sakakibara Y. 2015. Whole-genome sequencing and comparative genome analysis of Bacillus subtilis strains isolated from non-salted fermented soybean foods. PLoS One 10:1-21. DOI:10.1371/journal.pone.0141369
Kamada M, Hase S, Sato K, Toyoda A, Fujiyama A, Sakakibara Y. 2014. Whole genome complete resequencing of Bacillus subtilis Natto by combining long reads with high-quality short reads. PLoS One 9:1-12. DOI:10.1371/journal.pone.0109999
Kojima A, Ikehara S, Kamiya K, Kajita E, Sato Y, Kouda K, Tamaki J, Kagamimori S, Iki M. 2020. Natto intake is inversely associated with osteoporotic fracture risk in postmenopausal Japanese women. J Nutr 150:599-605. DOI:10.1093/jn/nxz292
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357-359. DOI:10.1038/nmeth.1923
Letunic I, Bork P. 2021. Interactive Tree of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Res 49:W293-296. DOI:10.1093/nar/gkab301
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinform 25:2078-2079. DOI:10.1093/bioinformatics/btp352
Li M, Zhang Z, Li S, Tian Z, Ma X. 2021. Study on the mechanism of production of ?-PGA and nattokinase in Bacillus subtilis Natto based on RNA-seq analysis. Microb Cell Fact 20:1-15. DOI:10.1186/s12934-021-01570-x
Lucy J, Raharjo PF, Elvina E, Florencia L, Susanti AI, Pinontoan R. 2019. Clot lysis activity of Bacillus subtilis G8 isolated from Japanese fermented natto soybeans. Appl Food Biotechnol 6:101-109. DOI:doi.org/10.22037/afb.v6i2.22479
Luo Z, Guo Y, Liu J, Qiu H, Zhao M, Zou W, Li S. 2016. Microbial synthesis of poly-?-glutamic acid: current progress, challenges, and future perspectives. Biotechnol Biofuels 9:1-12. DOI:10.1186/s13068-016-0537-7
Madeira F, Park Y mi, Lee J, Buso N, Gur T, Madhusoodanan N, Basutkar P, Tivey ARN, Potter SC, Finn RD, Lopez R. 2019. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res 47:W636-W641. DOI:10.1093/nar/gkz268
Meier-Kolthoff JP, Göker M. 2019. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10:1-10. DOI:10.1038/s41467-019-10210-3
Nagata C, Wada K, Tamura T, Konishi K, Goto Y, Koda S, Kawachi T, Tsuji M, Nakamura K. 2017. Dietary soy and natto intake and cardiovascular disease mortality in Japanese adults: The Takayama study. Am J Clin Nutr 105:426-431. DOI:10.3945/ajcn.116.137281
Nakamura T, Yamagata Y, Ichishima E. 1992. Nucleotide sequence of the subtilisin NAT gene, aprN, of Bacillus subtilis (natto). Biosci Biotechnol Biochem 56:1869-1871. DOI:10.1271/bbb.56.1869
Nishito Y, Osana Y, Hachiya T, Popendorf K, Toyoda A, Fujiyama A, Itaya M, Sakakibara Y. 2010. Whole genome assembly of a natto production strain Bacillus subtilis Natto from very short read data. BMC Genom 11:1-12. DOI:10.1186/1471-2164-11-243
Okonechnikov K, Conesa A, García-Alcalde F. 2015. Qualimap 2: Advanced multi-sample quality control for high-throughput sequencing data. Bioinform 32:292-294. DOI:10.1093/bioinformatics/btv566
Peng Y, Leung HCM, Yiu SM, Chin FYL. 2012. IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinform 28:1420-1428. DOI:10.1093/bioinformatics/bts174
Pinontoan R, Elvina, Sanjaya A, Jo J. 2021. Fibrinolytic characteristics of Bacillus subtilis G8 isolated from natto. Biosci Microbiota Food & Health 40:144-149. DOI:10.12938/bmfh.2020-071
Rissman AI, Mau B, Biehl BS, Darling AE, Glasner JD, Perna NT. 2009. Reordering contigs of draft genomes using the Mauve aligner. Bioinform 25:2071-2073. DOI:10.1093/bioinformatics/btp356
Rodriguez-R LM, Konstantinidis KT. 2016. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Prepr 4:2-10. DOI:10.7287/peerj.preprints.1900v1
Stanley NR, Lazazzera BA. 2005. Defining the genetic differences between wild and domestic strains of Bacillus subtilis that affect poly-?-dl-glutamic acid production and biofilm formation. Mol Microbiol 57:1143-1158. DOI:10.1111/j.1365-2958.2005.04746.x
Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. 2016. DFAST and DAGA: Web-based integrated genome annotation tools and resources. Biosci Microbiota Food & Health 35:173-184. DOI:10.12938/bmfh.16-003
Weng Y, Yao J, Sparks S, Wang KY. 2017. Nattokinase: An oral antithrombotic agent for the prevention of cardiovascular disease. Int J Mol Sci 18:1-13. DOI:10.3390/ijms18030523
Zhao X, Song J-L, Wang Q, Qian Y, Li G-J, Pang L. 2013. Comparisons of shuidouchi, natto, and cheonggukjang in their physicochemical properties, and antimutagenic and anticancer effects. Food Sci Biotechnol 22:1077-1084. DOI:10.1007/s10068-013-0186-6