Mining the genome of Bacillus velezensis FS26 for probiotic markers and secondary metabolites with antimicrobial properties against aquaculture pathogens

Sam-on, Muhamad Firdaus Syahmi; Mustafa, Shuhaimi; Hashim, Amalia Mohd; Yusof, Mohd Termizi; Zulkifly, Shahrizim; Malek, A; Roslan, Muhamad Akhmal Hakim; Asrore, Mohd Shaufi Mohd

doi:10.1016/j.micpath.2023.106161

Cited by 13 publications

(9 citation statements)

References 49 publications

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“…The genome sequence analysis of Bacillus velezensis TS5 also identified several stress-resistant genes including DnaK , OppA , Eno , nhaC , nhaX , and nhaK ( Supplementary Table 1 ). These findings are consistent with previous studies which have reported the presence of bile salt tolerance genes ( DnaK , OppA , and Eno ) in probiotic Bacillus velezensis FS26 ( Sam-On et al, 2023 ). The Na/H antiporter ( nhaC , nhaX ) and universal stress proteins ( nhaK ) play a crucial role in Na resistance and pH homeostasis, allowing the bacteria to survive in acidic conditions ( Fujisawa et al, 2005 ).…”

Section: Discussionsupporting

confidence: 93%

“…The genome of Bacillus velezensis TS5 contains three genes, lipoprotein signal peptidase ( LspA gene), glutamine binding periplasmic protein ( GlnH gene), and elongation factor Tu ( Tuf gene), which are also known as mucus adhesion domain protein (MucBPs) ( Supplementary Table 1 ). These proteins play a grucial role in host adhesion, automatic aggregation, and/or coaggregation with pathogenic bacteria ( Sam-On et al, 2023 ). The findings are consistent with previous studies which have reported the presence of similar MucBPs ( LspA , GlnH , and Tuf genes) in probiotic Bacillus velezensis FS26 ( Sam-On et al, 2023 ).…”

Section: Discussionmentioning

confidence: 99%

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Complete genome analysis of Bacillus velezensis TS5 and its potential as a probiotic strain in mice

Chen,

Zhou,

Duan

et al. 2023

Front. Microbiol.

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IntroductionIn recent years, a large number of studies have shown that Bacillus velezensis has the potential as an animal feed additive, and its potential probiotic properties have been gradually explored.MethodsIn this study, Illumina NovaSeq PE150 and Oxford Nanopore ONT sequencing platforms were used to sequence the genome of Bacillus velezensis TS5, a fiber-degrading strain isolated from Tibetan sheep. To further investigate the potential of B. velezensis TS5 as a probiotic strain, in vivo experiments were conducted using 40 five-week-old male specific pathogen-free C57BL/6J mice. The mice were randomly divided into four groups: high fiber diet control group (H group), high fiber diet probiotics group (HT group), low fiber diet control group (L group), and low fiber diet probiotics group (LT group). The H and HT groups were fed high-fiber diet (30%), while the L and LT groups were fed low-fiber diet (5%). The total bacteria amount in the vegetative forms of B. velezensis TS5 per mouse in the HT and LT groups was 1 × 109 CFU per day, mice in the H and L groups were given the same volume of sterile physiological saline daily by gavage, and the experiment period lasted for 8 weeks.ResultsThe complete genome sequencing results of B. velezensis TS5 showed that it contained 3,929,788 nucleotides with a GC content of 46.50%. The strain encoded 3,873 genes that partially related to stress resistance, adhesion, and antioxidants, as well as the production of secondary metabolites, digestive enzymes, and other beneficial nutrients. The genes of this bacterium were mainly involved in carbohydrate metabolism, amino acid metabolism, vitamin and cofactor metabolism, biological process, and molecular function, as revealed by KEGG and GO databases. The results of mouse tests showed that B. velezensis TS5 could improve intestinal digestive enzyme activity, liver antioxidant capacity, small intestine morphology, and cecum microbiota structure in mice.ConclusionThese findings confirmed the probiotic effects of B. velezensis TS5 isolated from Tibetan sheep feces and provided the theoretical basis for the clinical application and development of new feed additives.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Complete genome analysis of Bacillus velezensis TS5 and its potential as a probiotic strain in mice

Chen,

Zhou,

Duan

et al. 2023

Front. Microbiol.

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“…The adherence ability of probiotic strains to the host epithelium is due to their cell surface proteins. The isolate genomes consisted of 11 genes that may encode adhesion-related proteins, including maltose phosphorylase ( mdxK ), sporulation and biofilm formation ( spo0A ) [ 71 , 72 ], lipoprotein signal peptidase I ( lspA ), elongation factor Tu ( tuf ) [ 73 , 74 , 75 ], sortase A ( srtA ) [ 76 , 77 ], and putative glycosyltransferase ( EpsH ) [ 78 , 79 , 80 , 81 ]. Another gene, xylA , linked with gut persistence was also found [ 80 , 82 ].…”

Section: Resultsmentioning

confidence: 99%

In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates

Bin Hafeez,

Pełka,

Worobo

et al. 2024

IJMS

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Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites.

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“…10 Fengycin is also widely used in environmental remediation 11 and biological control in aquaculture. 12 The application of fengycin is hindered by its low yield and high cost. At present, the research on improving fengycin production is focused mainly on fermentation optimization and endogenous regulation.…”

mentioning

confidence: 99%

“…Under the influence of fengycin, microbial cell membranes become unstable and rupture . Fengycin is also widely used in environmental remediation and biological control in aquaculture …”

mentioning

confidence: 99%

An Engineered Microbial Consortium Provides Precursors for Fengycin Production by Bacillus subtilis

Wei,

Gao,

Ding

et al. 2024

J. Nat. Prod.

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Fengycin has great potential for applications in biological control because of its biosafety and degradability. In this study, the addition of exogenous precursors increased fengycin production by Bacillus subtilis. Corynebacterium glutamicum was engineered to produce high levels of precursors (Thr, Pro, Val, and Ile) to promote the biosynthesis of fengycin. Furthermore, recombinant C. glutamicum and Yarrowia lipolytica providing amino acid and fatty acid precursors were co-cultured to improve fengycin production by B. subtilis in a threestrain artificial consortium, in which fengycin production was 2100 mg• L −1 . In addition, fengycin production by the consortium in a 5 L bioreactor reached 3290 mg•L −1 . Fengycin had a significant antifungal effect on Rhizoctonia solani, which illustrates its potential as a food preservative. Taken together, this work provides a new strategy for improving fengycin production by a microbial consortium and metabolic engineering.

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Mining the genome of Bacillus velezensis FS26 for probiotic markers and secondary metabolites with antimicrobial properties against aquaculture pathogens

Cited by 13 publications

References 49 publications

Complete genome analysis of Bacillus velezensis TS5 and its potential as a probiotic strain in mice

Complete genome analysis of Bacillus velezensis TS5 and its potential as a probiotic strain in mice

In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates

An Engineered Microbial Consortium Provides Precursors for Fengycin Production by Bacillus subtilis

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