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Peerzade IJ, Mutturi S, Halami PM. Improved production of RNA-inhibiting antimicrobial peptide by Bacillus licheniformis MCC 2514 facilitated by a genetic algorithm optimized medium. Bioprocess Biosyst Eng 2024; 47:683-695. [PMID: 38521865 DOI: 10.1007/s00449-024-02998-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
One of the significant challenges during the purification and characterization of antimicrobial peptides (AMPs) from Bacillus sp. is the interference of unutilized peptides from complex medium components during analytical procedures. In this study, a semi-synthetic medium was devised to overcome this challenge. Using a genetic algorithm, the production medium of AMP is optimized. The parent organism, Bacillus licheniformis MCC2514, produces AMP in very small quantities. This AMP is known to inhibit RNA biosynthesis. The findings revealed that lactose, NH4Cl and NaNO3 were crucial medium constituents for enhanced AMP synthesis. The potency of the AMP produced was studied using bacterium, Kocuria rhizophila ATCC 9341. The AMP produced from the optimized medium was eightfold higher than that produced from the unoptimized medium. Furthermore, activity was increased by 1.5-fold when cultivation conditions were standardized using the optimized medium. Later, AMP was produced in a 5 L bioreactor under controlled conditions, which led to similar results as those of shake-flask production. The mode of action of optimally produced AMP was confirmed to be inhibition of RNA biosynthesis. Here, we demonstrate that improved production of AMP is possible with the developed semi-synthetic medium recipe and could help further AMP production in an industrial setup.
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Affiliation(s)
- Ishrat Jahan Peerzade
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
| | - Sarma Mutturi
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
| | - Prakash M Halami
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India.
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Characterization of dual bacteriocins producing Bacillus subtilis SC3.7 isolated from fermented food. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sharma BR, Jayant D, Rajshee K, Singh Y, Halami PM. Distribution and Diversity of Nisin Producing LAB in Fermented Food. Curr Microbiol 2021; 78:3430-3438. [PMID: 34255153 DOI: 10.1007/s00284-021-02593-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 06/11/2021] [Indexed: 10/20/2022]
Abstract
An attempt was made, to characterize natural antibiotics or lantibiotics from unconventional sources and its antibacterial spectrum against food borne pathogens and drug resistant bacteria. Six different traditional fermented foods i.e., fermented fish, fermented soybeans, Soibum (fermented bamboo shoots), milk, idly and dosa batter were used for the isolation of bacteriocin producing Lactic acid bacteria (LAB). Among all bacterial cultures isolated from the various sources, 129 cultures have found to produce antimicrobial compounds. Nisin specific reporter bacteria was utilized as biosensor to identify the Nisin like bacteriocin, where 10 cultures found to be positive Nisin producer. Identified Nisin like bacteriocin was partially concentrated by using ammonium sulphate followed by butanol extraction. Minimum inhibitory concentration (MIC) was analyzed against food borne pathogen and drug resistant bacteria. MIC of partially purified Nisin (pp-Nisin) of all the LAB isolates against food-borne pathogens are ranged between 0.5 and 92 µg/ml respected to various Gram-positive bacteria. Similarly, the drug resistant bacteria were also inhibited by pp-Nisin (MIC ranged between 15 and 175 µg/ml). All samples of ppnisin exhibited auto induction ability. Taxonomic identification of the nisin producers was done by whole genome sequencing which reveals that cultures belongs to Lactococcus lactis ssp. lactis. Also it was found that Lactococcus lactis ssp. lactis C2d and Lactococcus lactis ssp. lactis SP2C4 harbor nisA gene and Lactococcus lactis ssp. lactis FS2 (L. lactis FS2) harbor nisQ gene. The finding of this study highlights the first case of L. lactis FS2 isolated from fermented fish harbor nisQ gene. Antibacterial activity of pp-Nisin against drug resistant LAB is also reported.
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Affiliation(s)
- Basista Rabina Sharma
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, 570020, India
| | - Dharana Jayant
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, 570020, India
| | - Kumari Rajshee
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, 570020, India
| | - Yashika Singh
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, 570020, India
| | - Prakash M Halami
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, 570020, India.
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Goel A, Halami PM, Tamang JP. Genome Analysis of Lactobacillus plantarum Isolated From Some Indian Fermented Foods for Bacteriocin Production and Probiotic Marker Genes. Front Microbiol 2020; 11:40. [PMID: 32063893 PMCID: PMC7000354 DOI: 10.3389/fmicb.2020.00040] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/09/2020] [Indexed: 01/09/2023] Open
Abstract
In this study, Lactobacillus plantarum strain DHCU70 isolated from dahi, a fermented milk product and L. plantarum strain DKP1 isolated from kinema, a fermented soybean food of India, respectively were evaluated for their bacteriocin production and probiotic properties. Both strains of L. plantarum (DHCU70 and DKP1) were found to have potent antimicrobial activity against Kocuria rhizophila ATCC 9341. Bacteriocin produced by L. plantarum strains DHCU70 and DKP1 did not exhibit inhibition of cell wall, DNA and fatty acids biosynthesis mechanisms as evaluated by whole cell reporter assays. We characterized the bacteriocin encoding genes in L. plantarum strains DHCU70 and DKP1 by whole genome sequence which consisted of a single and circular chromosome with genome size of 3.38 Mb (GC content of 44.3%) and 3.39 Mb, respectively and a GC content of 44.3%. L. plantarum DHCU70 has 3252 number of protein encoding genes comprising 89 number of RNA genes (69tRNA, 16rRNA, 4nc RNA) whereas L. plantarum DKP1 has total of 3277 number of protein encoding genes with 89 number. of RNA genes (69tRNA, 16S rRNA, 4nc RNA). Analysis revealed the presence of 20.5 kb long and 23 numbers of plantaricin encoding locus (pln locus) for production of antimicrobial compound. BAGEL analysis has shown that the pln locus of both the strains of L. plantarum showed maximum sequence similarity with plantaricin NC8 of L. plantarum NC8, originally isolated from grass silage. Annotated whole genome sequence of both strains DHCU70 and DKP1 was analyzed for the presence of probiotic marker genes. The probiotic properties of these strains of were also evaluated in vitro. Due to the presence of genes responsible for antimicrobial activity and probiotic properties, both strains of L. plantarum may be considered as a suitable probiotic candidate in food industry.
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Affiliation(s)
- Aditi Goel
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru, India
| | - Prakash M. Halami
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru, India
| | - Jyoti Prakash Tamang
- DBT-AIST International Centre for Translational and Environmental Research and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
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Vadakedath N, Halami PM. Characterization and mode of action of a potent bio-preservative from food-gradeBacillus licheniformisMCC 2016. Prep Biochem Biotechnol 2019; 49:334-343. [DOI: 10.1080/10826068.2019.1566141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Nithya Vadakedath
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysore, India
| | - Prakash M. Halami
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysore, India
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Diversity in the antibacterial potential of probiotic cultures Bacillus licheniformis MCC2514 and Bacillus licheniformis MCC2512. Res Microbiol 2015; 166:546-54. [PMID: 26100933 DOI: 10.1016/j.resmic.2015.06.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/11/2015] [Accepted: 06/01/2015] [Indexed: 11/21/2022]
Abstract
The aim of the present study was to investigate the characteristic diversity and stability of antimicrobial compounds produced by two probiotic strains of Bacillus licheniformis (MCC2514 and MCC2512). Antimicrobial compounds from the two strains notably varied, related to stability and potency. The inhibitory spectrum of B. licheniformis MCC2512 was higher than MCC2514, but, related to the effect on Micrococcus luteus ATCC9341, MCC2514 (LD50 = 450 AU ml(-1)) was more potent than MCC2512 (LD50 = 750 AU ml(-1)). The compounds were thermo-resistant and stable at a wide range of pH and exhibited considerable resistance to digestive enzymes and bile salts (anionic biological detergents), contributing to their appropriate application in various food systems. The isolate B. licheniformis MCC2512 gave a positive response to Bacillus subtilis-based biosensors BSF2470 and BS168.BS2, confirming the mode of action on the cell wall and subtilin-type, respectively. For B. licheniformis MCC2514, the mode of action was characterized by constructing B. subtilis reporters that interfered in five major biosynthetic pathways, i.e., biosynthesis of DNA, RNA, protein, the cell wall and fatty acids. B. licheniformis MCC2514 responded to the yvgS reporter, indicating it as an RNA synthesis inhibitor. Overall, the investigation reveals variability of the antimicrobial compounds from B. licheniformis of different origins and for their possible application as biopreservative agents.
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Ait Kaki A, Kacem Chaouche N, Dehimat L, Milet A, Youcef-Ali M, Ongena M, Thonart P. Biocontrol and Plant Growth Promotion Characterization of Bacillus Species Isolated from Calendula officinalis Rhizosphere. Indian J Microbiol 2013; 53:447-52. [PMID: 24426149 DOI: 10.1007/s12088-013-0395-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 03/19/2013] [Indexed: 11/28/2022] Open
Abstract
The phenotypic and genotypic diversity of the plant growth promoting Bacillus genus have been widely investigated in the rhizosphere of various agricultural crops. However, to our knowledge this is the first report on the Bacillus species isolated from the rhizosphere of Calendula officinalis. 15 % of the isolated bacteria were screened for their important antifungal activity against Fusarium oxysporum, Botrytis cinerea, Aspergillus niger, Cladosporium cucumerinium and Alternaria alternata. The bacteria identification based on 16S r-RNA and gyrase-A genes analysis, revealed strains closely related to Bacillus amyloliquefaciens, B. velezensis, B. subtilis sub sp spizezenii and Paenibacillus polymyxa species. The electro-spray mass spectrometry coupled to liquid chromatography (ESI-LC MS) analysis showed that most of the Bacillus isolates produced the three lipopeptides families. However, the P. polymyxa (18SRTS) didn't produce any type of lipopeptides. All the tested Bacillus isolates produced cellulase but the protease activity was observed only in the B. amyloliquefaciens species (9SRTS). The Salkowsky colorimetric test showed that the screened bacteria synthesized 6-52 μg/ml of indole 3 acetic acid. These bacteria produced siderophores with more than 10 mm wide orange zones on chromazurol S. The greenhouse experiment using a naturally infested soil with Sclerotonia sclerotiorum showed that the B. amyloliquefaciens (9SRTS) had no significant (P > 0.05) effect on the pre-germination of the chickpea seeds. However, it increased the size of the chickpea plants and reduced the stem rot disease (P < 0.05).These results suggested that the Bacillus strains isolated in this work may be further used as bioinoculants to improve the production of C. officinalis and other crop systems.
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Affiliation(s)
- Asma Ait Kaki
- Centre Wallon de Biologie Industrielle, Université de Liège, B40-Sart-Tilman, 4000 Liège, Belgium ; Laboratoire de Mycologie, Biotechnologie et de l'Activité Antimicrobienne, Département de Biochimie-Microbiologie, Université Mentouri de Constantine, Aein Elbey, 25017 Constantine, Algeria
| | - Noreddine Kacem Chaouche
- Laboratoire de Mycologie, Biotechnologie et de l'Activité Antimicrobienne, Département de Biochimie-Microbiologie, Université Mentouri de Constantine, Aein Elbey, 25017 Constantine, Algeria
| | - Laid Dehimat
- Laboratoire de Mycologie, Biotechnologie et de l'Activité Antimicrobienne, Département de Biochimie-Microbiologie, Université Mentouri de Constantine, Aein Elbey, 25017 Constantine, Algeria
| | - Asma Milet
- Laboratoire de Mycologie, Biotechnologie et de l'Activité Antimicrobienne, Département de Biochimie-Microbiologie, Université Mentouri de Constantine, Aein Elbey, 25017 Constantine, Algeria
| | - Mounia Youcef-Ali
- Laboratoire de Mycologie, Biotechnologie et de l'Activité Antimicrobienne, Département de Biochimie-Microbiologie, Université Mentouri de Constantine, Aein Elbey, 25017 Constantine, Algeria
| | - Marc Ongena
- Centre Wallon de Biologie Industrielle, Université de Liège, B40-Sart-Tilman, 4000 Liège, Belgium
| | - Philippe Thonart
- Centre Wallon de Biologie Industrielle, Université de Liège, B40-Sart-Tilman, 4000 Liège, Belgium
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