Functional Annotation Genome Unravels Potential Probiotic Bacillus velezensis Strain KMU01 from Traditional Korean Fermented Kimchi

Abstract

Bacillus velezensis strain KMU01 showing γ-glutamyltransferase activity as a probiotic candidate was isolated from kimchi. However, the genetic information on strain KMU01 was not clear. Therefore, the current investigation was undertaken to prove the probiotic traits of B. velezensis strain KMU01 through genomic analysis. Genomic analysis revealed that strain KMU01 did not encode enterotoxin genes and acquired antibiotic resistance genes. Strain KMU01 genome possessed survivability traits under extreme conditions such as in the presence of gastric acid, as well as several probiotic traits such as intestinal epithelium adhesion and the production of thiamine and essential amino acids. Potential genes for human health enhancement such as those for γ-glutamyltransferase, nattokinase, and bacteriocin production were also identified in the genome. As a starter candidate for food fermentation, the genome of KMU01 encoded for protease, amylase, and lipase genes. The complete genomic sequence of KMU01 will contribute to our understanding of the genetic basis of probiotic properties and allow for the assessment of the effectiveness of this strain as a starter or probiotic for use in the food industry.

Functional Genomic Insights into Probiotic Bacillus siamensis Strain B28 from Traditional Korean Fermented Kimchi

“…However, strain B28 did not exhibit resistance to lincomycin or tetracycline (Figure S4). These genes have previously been identified in the genomes of several strains that did not show resistance to the respective antibiotics [15,42], and the genes were detected on the chromosomes of B. amyloliquefaciens and B. velezensis, not on plasmids. These results imply that these were not acquired antibiotic resistance genes (Table 2).…”

“…have been used in the preparation of diverse fermented soybean products in northeast Asia for many centuries [14]. Furthermore, some Bacillus strains exhibit antibacterial activity against food pathogenic bacteria [15,16], anticancer effects on human colon cancer cells [17], and probiotic properties in humans and animals [18].…”

“…However, B. polyfermenticus has not yet been placed in the taxonomy database of the National Center for Biotechnology Information at June 2021 (NCBI; http: //ncbi.nlm.nih.gov/Taxonomy) or in the List of Prokaryotic Names with Standing in Nomenclature [20]. Recently, several B. polyfermenticus strains have been reclassified: B. polyfermenticus GF423 was renamed B. velezensis variant polyfermenticus GF423 based on genome sequencing [21], and B. polyfermenticus KMU01 was reclassified as B. velezensis KMU01 [15]. Therefore, in this study, we examined the classification of strain B28 based on its whole genome sequence.…”

Complete Genome Sequencing and Comparative Genomics of Three Potential Probiotic Strains, Lacticaseibacillus casei FBL6, Lacticaseibacillus chiayiensis FBL7, and Lacticaseibacillus zeae FBL8

“…In the three genomes, most coding genes were classified for general function prediction only (R, 13.11-13.43%), carbohydrate transport and metabolism (G, 11.68-13.01%), transcription (K, 8.87-9.19%), and amino acid transport and metabolism (E, 8.78-8.97%) (Supplementary Figure 1). The high proportion of genes involved in carbohydrate and amino acid metabolism indicates that three strains might utilize and degrade a wide range of carbohydrates and proteins (Heo et al, 2021).…”

“…The FBL6 genome harbored the eight genes (locus_00683 to locus_00690), which encodes F0F1 ATP synthetase, and the gene locus_01410, which encodes the cholylglycine hydrolase; these proteins are associated with resistance to low pH and bile. Cholylglycine hydrolase is responsible for converting conjugated bile acid into free bile acid and confers probiotics in the gastrointestinal tract (Heo et al, 2021). FBL6 genome possessed genes encoding heat stress proteins, including molecular chaperone (locus_02010), dnaK (locus_00321), GroES (locus_02686), GroEL (locus_02687), and heat shock protein GrpE (locus_00320).…”