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Azhar M, Yousaf M, Maher S, Fatmi MQ. Discovering Potential Bacteriocins Against Pseudomonas fragi: a Subtractive Proteomics and Molecular Dynamic Simulation Study for Food Preservation. Appl Biochem Biotechnol 2024; 196:2851-2868. [PMID: 37103735 DOI: 10.1007/s12010-023-04509-7] [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] [Accepted: 04/11/2023] [Indexed: 04/28/2023]
Abstract
Food preservation is a schematic and scientific procedure employed for the maintenance and improvement of food's quality, shelf life, and nutritional value. Although, on one hand, ancient conventional methods such as freezing, pasteurization, canning, and chemical methods have the potential to lengthen the shelf life of edible substances, but on the other hand, they can deteriorate its nutritional value as well. Present research focuses on the identification of promising bacteriocins against Pseudomonas fragi via subtractive proteomics pipeline as an alternative approach for food preservation. Bacteriocins are small peptides produced by certain microbes to naturally defend themselves by destroying other closely related bacteria residing in their neighborhood. P. fragi lies among the most notable microbes responsible for the elicitation of food spoilage. Due to increasing emergence and prevalence of multidrug resistance bacteria, there is a need to unravel novel drug targets, crucially involved in food decay process. Based on subtractive scrutinization, UDP-N-acetylglucosamine O-acyltransferase (LpxA) was chosen as promising therapeutic protein target that could play a significant role in progression of food spoilage. Subtilosin A, thuricin-CD, and mutacin B-NY266 were found as the most robust inhibitors of LpxA according to the molecular docking assay results. Molecular dynamic simulations and binding energy calculations via MM/PBSA method of LpxA and three top hit docked complexes, i.e., LpxA-subtilosin A, LpxA-thuricin-CD, and LpxA-mutacin B-NY266, revealed stability throughout simulations and ensured that shortlisted bacteriocins had strong affinity for LpxA.
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Affiliation(s)
- Maria Azhar
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan
| | - Maha Yousaf
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan
| | - Saima Maher
- Department of Chemistry, Sardar Bahadur Khan Women's University, Quetta, Pakistan
| | - M Qaiser Fatmi
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan.
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2
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Choeisoongnern T, Chaiyasut C, Sivamaruthi BS, Makhamrueang N, Peerajan S, Sirilun S, Sittiprapaporn P. Bacteriocin-Producing Enterococcus faecium OV3-6 as a Bio-Preservative Agent to Produce Fermented Houttuynia cordata Thunb. Beverages: A Preliminary Study. Foods 2023; 12:3520. [PMID: 37835173 PMCID: PMC10572304 DOI: 10.3390/foods12193520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Microbial contamination affects the quality of the fermented Houttuynia cordata Thunb. (H. cordata) beverage (FHB). The present study aimed to assess the bio-preservative property of Enterococcus faecium OV3-6 (E. faecium OV3-6) during the production of FHB. The antimicrobial activity against Escherichia coli, Salmonella, Bacillus cereus, and Staphylococcus aureus and the survival of E. faecium OV3-6 were studied. Then, FHB fermentation was performed with different preservatives (non-preservative, E. faecium OV3-6, cell-free supernatant of E. faecium OV3-6, and nisin) with and without representative pathogens. The maximum antimicrobial activity against S. aureus and B. cereus was observed after 18 h of cultivation in an MRS medium. E. faecium OV3-6 was used as a starter to produce the FHB, and the strain survived up to 48 h in the fermented beverage. E. faecium OV3-6 and its cell-free supernatant inhibited the growth of E. coli, Salmonella, B. cereus, and S. aureus in the stimulated FHB. The non-preservatives and nisin-containing FHB showed inhibition against Gram-positive pathogens. The FHB treated with E. faecium OV3-6 was rich in lactic acid bacteria, and the product was at an acceptable level of pH (less than 4.3). Certain limitations were identified in the study, such as lack of nutritional, metabolomics analysis, and safety and consumer acceptability of FHB. The results suggested that E. faecium OV3-6 could be used as a bio-preservative to produce fermented plant beverages (FPBs).
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Affiliation(s)
- Thiwanya Choeisoongnern
- Neuropsychological Research Laboratory, Neuroscience Research Center, School of Anti-Aging and Regenerative Medicine, Mae Fah Luang University, Bangkok 10110, Thailand
| | - Chaiyavat Chaiyasut
- Innovation Center for Holistic Health, Nutraceuticals and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand; (C.C.); (B.S.S.)
| | - Bhagavathi Sundaram Sivamaruthi
- Innovation Center for Holistic Health, Nutraceuticals and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand; (C.C.); (B.S.S.)
- Office of Research Administration, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Netnapa Makhamrueang
- Office of Research Administration, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | | | - Sasithorn Sirilun
- Innovation Center for Holistic Health, Nutraceuticals and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand; (C.C.); (B.S.S.)
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Phakkharawat Sittiprapaporn
- Neuropsychological Research Laboratory, Neuroscience Research Center, School of Anti-Aging and Regenerative Medicine, Mae Fah Luang University, Bangkok 10110, Thailand
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Hameed A, Anwar MJ, Perveen S, Amir M, Naeem I, Imran M, Hussain M, Ahmad I, Afzal MI, Inayat S, Awuchi CG. Functional, industrial and therapeutic applications of dairy waste materials. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2023; 26:1470-1496. [DOI: 10.1080/10942912.2023.2213854] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/09/2023] [Indexed: 05/18/2024]
Affiliation(s)
- Aneela Hameed
- Faculty of Food Science and Nutrition, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Muhammad Junaid Anwar
- Faculty of Food Science and Nutrition, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Saima Perveen
- Faculty of Food Science and Nutrition, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Muhammad Amir
- Faculty of Food Science and Nutrition, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Iqra Naeem
- Faculty of Food Science and Nutrition, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Muhammad Imran
- Department of food science and technology, University of Narowal-Pakistan, Narowal, Pakistan
| | - Muzzamal Hussain
- Department of Food Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ishtiaque Ahmad
- Department of Dairy Technology, University of Veterinary & Animal Sciences, Lahore, Pakistan
| | - Muhamad Inam Afzal
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Saima Inayat
- Department of Dairy Technology, University of Veterinary & Animal Sciences, Lahore, Pakistan
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Biki SP, Mahmud S, Akhter S, Rahman MH, Ahmed M. Bacteriocin production by
Lactococcus lactis
LL‐HSTU‐FPP
strain isolated from fermented rice and evaluation of the biopreservation potentiality of bacteriocin on shrimp. J Food Saf 2023. [DOI: 10.1111/jfs.13042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Suchi Parvin Biki
- Department of Food Processing and Preservation Hajee Mohammad Danesh Science & Technology University Dinajpur Bangladesh
| | - Shobuz Mahmud
- Department of Food Processing and Preservation Hajee Mohammad Danesh Science & Technology University Dinajpur Bangladesh
| | - Sumaia Akhter
- Department of Food Processing and Preservation Hajee Mohammad Danesh Science & Technology University Dinajpur Bangladesh
| | - Md. Hassanur Rahman
- Department of Horticulture Hajee Mohammad Danesh Science and Technology University Dinajp Bangladesh
| | - Maruf Ahmed
- Department of Food Processing and Preservation Hajee Mohammad Danesh Science & Technology University Dinajpur Bangladesh
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5
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Immunomodulatory action of Lactococcuslactis. J Biosci Bioeng 2023; 135:1-9. [PMID: 36428209 DOI: 10.1016/j.jbiosc.2022.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/07/2022] [Accepted: 10/24/2022] [Indexed: 11/24/2022]
Abstract
Fermented foods are gaining popularity due to health-promoting properties with high levels of nutrients, phytochemicals, bioactive compounds, and probiotic microorganisms. Due to its unique fermentation process, Lactococcus lactis plays a key role in the food business, notably in the manufacturing of dairy products. The superior biological activities of L. lactis in these functional foods include anti-inflammatory and immunomodulatory capabilities. L. lactis boosted growth performance, controlled amino acid profiles, intestinal immunology, and microbiota. Besides that, the administration of L. lactis increased the rate of infection clearance. Innate and acquired immune responses would be upregulated in both local and systemic compartments, resulting in these consequences. L. lactis is often employed in the food sector and is currently being exploited as a delivery vehicle for biological research. These bacteria are being eyed as potential candidates for biotechnological applications. With this in mind, we reviewed the immunomodulatory effects of different L. lactis strains.
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Lei W, Hao L, You S, Yao H, Liu C, Zhou H. Partial purification and application of a bacteriocin produced by probiotic Lactococcus lactis C15 isolated from raw milk. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Cultivation of Lactic Acid Bacteria and Evaluation of the Antimicrobial Potential of Partially Purified Bacteriocin-like Inhibitory Substances against Cariogenic and Food Pathogens. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8080400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
One of the major challenges in the pharmaceutical industry is the search for new antimicrobial compounds that can replace antibiotics. Lactic acid bacteria (LAB) can produce bacteriocin-like inhibitory substances (BLIS) that have a bacteriostatic or bactericidal effect against different bacterial genera, including those responsible for dental caries. Among the pathological processes of microbial etiology, the dental caries stands out, whose main pathogenic agent is the species Streptococcus mutans, present in about 80–90% of the oral cavity. In this context, this study aimed to produce and semi-purify BLIS from Lactobacillus plantarum ST16 Pa, Bifidobacteriumlactis BL 04, Lactococcus lactis CECT-4434 and Lactobacillus lactis 27 as well as to assess their antimicrobial potential against important dental caries causing pathogens like S. mutans UA159, Listeria innocua 2711, Carnobacterium maltaromaticum CECT 4020, Staphylococcus aureus CECT 239, and Escherichia coli ATCC 25922. While BLIS from L. plantarum ST16 Pa and L. lactis CECT-4434 were able to inhibit the growth only of S. mutans UA159, that which was produced by B. lactis BL 04 did so against all bioindicator strains; therefore, this suggests that its application could be important in the control of cariogenic microorganisms.
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8
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Production and fermentation characteristics of antifungal peptides by synergistic interactions with Lactobacillus paracasei and Propionibacterium freudenii in supplemented whey protein formulations. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Abouloifa H, Hasnaoui I, Ben Slima S, Rokni Y, Gaamouche S, Trabelsi I, Bellaouchi R, Ghabbour N, Ben Salah R, Jaouadi B, Saalaoui E, Asehraou A. Bio-preservation Effect of Probiotic Lactiplantibacillus plantarum S61 Against Rhodotorula glutinis and Listeria monocytogenes in Poultry Meat. Curr Microbiol 2022; 79:232. [PMID: 35767082 DOI: 10.1007/s00284-022-02923-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/03/2022] [Indexed: 11/25/2022]
Abstract
The objective of this work is the study of the antifungal and antibacterial activity of Lactiplantibacillus plantarum S61 strains, isolated from traditional fermenting green olives against Rhodotorula glutinis UMP 22 and Listeria monocytogenes ATCC 19117, and its application in meat as bio-preservative agent. The cell-free supernatant (CFS) of Lpb. plantarum S61 shows high inhibition zones, which are 22.45 ± 0.49 and 17.75 ± 0.35 mm, against Rhodotorula glutinis and Listeria monocytogenes. The minimum fungicidal and bactericidal concentrations of the CFS obtained are 8% (v/v) and 10% (v/v), respectively. The competition assay, realized in liquid medium by co-culture of Lpb. plantarum S61 with Rho Rhodotorula glutinis and L. monocytogenes, led to inhibition percentages of 77.72% and 89.52%, respectively. However, the antimicrobial activity of Lpb. plantarum S61 was revealed a proteinaceous nature. Lpb. plantarum S61 strain allowed the reduction of L. monocytogenes in minced poultry meat during 7 days of storage at 4 °C. In addition, Lpb. plantarum S61 improved the physicochemical and color parameters of poultry minced meat. Lpb. plantarum S61 and/or its antimicrobial compounds can be applied as bio-preservative agent in meat product and food industry.
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Affiliation(s)
- Houssam Abouloifa
- Laboratory of Bioressource, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed Premier University, 60 000, Oujda, Morocco.
- Research Unit of Microbiology, Biomolecules and Biotechnology, Laboratory of Chemistry-Physics and Biotechnology of Molecules and Materials, Faculty of Sciences and Techniques, Mohammedia, Hassan II University of Casablanca, Mohammédia, Morocco.
| | - Ismail Hasnaoui
- Laboratory of Bioressource, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed Premier University, 60 000, Oujda, Morocco
| | - Sirine Ben Slima
- Laboratory of Microorganisms and Biomolecules, Centre of Biotechnology of Sfax, BP: 1177, 3018, Sfax, Tunisia
| | - Yahya Rokni
- Laboratory of Bioressource, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed Premier University, 60 000, Oujda, Morocco
- Research Unit Bioprocess and Biointerfaces, Laboratory of Industrial Engineering and Surface Engineering, National School of Applied Sciences, Sultan Moulay Slimane University, Mghila, 23000, Beni Mellal, Morocco
| | - Sara Gaamouche
- Laboratory of Bioressource, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed Premier University, 60 000, Oujda, Morocco
| | - Imen Trabelsi
- Laboratory of Microorganisms and Biomolecules, Centre of Biotechnology of Sfax, BP: 1177, 3018, Sfax, Tunisia
| | - Reda Bellaouchi
- Laboratory of Bioressource, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed Premier University, 60 000, Oujda, Morocco
| | - Nabil Ghabbour
- Laboratory of Bioressource, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed Premier University, 60 000, Oujda, Morocco
- Laboratory of Natural Resources and Environment, Polydisciplinary Faculty of Taza, Sidi Mohamed Ben Abdellah University, B. P 1223, Taza, Morocco
| | - Riadh Ben Salah
- Laboratory of Microorganisms and Biomolecules, Centre of Biotechnology of Sfax, BP: 1177, 3018, Sfax, Tunisia
| | - Bassem Jaouadi
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road Sidi Mansour 6 km, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Ennouamane Saalaoui
- Laboratory of Bioressource, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed Premier University, 60 000, Oujda, Morocco
| | - Abdeslam Asehraou
- Laboratory of Bioressource, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed Premier University, 60 000, Oujda, Morocco
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10
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Darbandi A, Asadi A, Mahdizade Ari M, Ohadi E, Talebi M, Halaj Zadeh M, Darb Emamie A, Ghanavati R, Kakanj M. Bacteriocins: Properties and potential use as antimicrobials. J Clin Lab Anal 2021; 36:e24093. [PMID: 34851542 PMCID: PMC8761470 DOI: 10.1002/jcla.24093] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/03/2021] [Accepted: 10/24/2021] [Indexed: 12/12/2022] Open
Abstract
A variety of bacteriocins originate from lactic acid bacteria, which have recently been modified by scientists. Many strains of lactic acid bacteria related to food groups could produce bacteriocins or antibacterial proteins highly effective against foodborne pathogens such as Staphylococcus aureus, Pseudomonas fluorescens, P. aeruginosa, Salmonella typhi, Shigella flexneri, Listeria monocytogenes, Escherichia coli O157:H7, and Clostridium botulinum. A wide range of bacteria belonging primarily to the genera Bifidobacterium and Lactobacillus have been characterized with different health‐promoting attributes. Extensive studies and in‐depth understanding of these antimicrobials mechanisms of action could enable scientists to determine their production in specific probiotic lactic acid bacteria, as they are potentially crucial for the final preservation of functional foods or for medicinal applications. In this review study, the structure, classification, mode of operation, safety, and antibacterial properties of bacteriocins as well as their effect on foodborne pathogens and antibiotic‐resistant bacteria were extensively studied.
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Affiliation(s)
- Atieh Darbandi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Arezoo Asadi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Marzieh Mahdizade Ari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Elnaz Ohadi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Malihe Talebi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Masoume Halaj Zadeh
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Darb Emamie
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Maryam Kakanj
- Food and Drug Laboratory Research Center, Food and Drug Administration, MOH&ME, Tehran, Iran
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Kirtonia K, Salauddin M, Bharadwaj KK, Pati S, Dey A, Shariati MA, Tilak VK, Kuznetsova E, Sarkar T. Bacteriocin: A new strategic antibiofilm agent in food industries. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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12
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Flynn J, Ryan A, Hudson SP. Pre-formulation and delivery strategies for the development of bacteriocins as next generation antibiotics. Eur J Pharm Biopharm 2021; 165:149-163. [PMID: 34020021 DOI: 10.1016/j.ejpb.2021.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/06/2021] [Accepted: 05/12/2021] [Indexed: 10/21/2022]
Abstract
Bacteriocins, a class of antimicrobial peptide produced by bacteria, may offer a potential alternative to traditional antibiotics, an important step towards mitigating the ever-increasing antimicrobial resistance crisis. They are active against a range of clinically relevant Gram-positive and Gram-negative bacteria. Bacteriocins have been discussed in the literature for over a century. Although they are used as preservatives in food, no medicine based on their antimicrobial activity exists on the market today. In order to formulate them into clinical antibiotics, pre-formulation studies on their biophysical and physicochemical properties that will influence their activity in vivo and their stability during manufacture must be elucidated. Thermal, pH and enzymatic stability of bacteriocins are commonly studied and regularly reported in the literature. Solubility, permeability and aggregation properties on the other hand are less frequently reported for many bacteriocins, which may contribute to their poor clinical progression. Promising cytotoxicity studies report that bacteriocins exhibit few cytotoxic effects on a variety of mammalian cell lines, at active concentrations. This review highlights the lack of quantitative data and in many cases even qualitative data, on bacteriocins' solubility, stability, aggregation, permeability and cytotoxicity. The formulation strategies that have been explored to date, proposed routes of administration, trends in in vitro/in vivo behaviour and efforts in clinical development are discussed. The future promise of bacteriocins as a new generation of antibiotics may require tailored local delivery strategies to fulfil their potential as a force to combat antimicrobial-resistant bacterial infections.
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Affiliation(s)
- James Flynn
- Department of Chemical Sciences, SSPC, the SFI Research Centre for Pharmaceuticals, Bernal Institute, University of Limerick, Ireland
| | - Aoibhín Ryan
- Department of Chemical Sciences, SSPC, the SFI Research Centre for Pharmaceuticals, Bernal Institute, University of Limerick, Ireland
| | - Sarah P Hudson
- Department of Chemical Sciences, SSPC, the SFI Research Centre for Pharmaceuticals, Bernal Institute, University of Limerick, Ireland.
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Solcova M, Demnerova K, Purkrtova S. Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts. Microorganisms 2021; 9:microorganisms9050937. [PMID: 33925711 PMCID: PMC8146283 DOI: 10.3390/microorganisms9050937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 01/11/2023] Open
Abstract
The aspiration these days is to apply rapid methods for parallel analysis of bacteriome and resistome of food samples to increase food safety and prevent antibiotic resistance genes (ARGs) spreading. In this work, we used nanopore sequencing (NS) to determine the diversity and dynamics of the microbiome and resistome in two types of bean sprouts. We proved that NS provided an easy, quick, and reliable way to identify the microbiome and resistome of a food sample also. The species diversity obtained by NS and by cultivation methods with MALDI-TOF MS identification was comparable. In both samples, before and after cultivation (30 °C, 48 h), the dominant part of bacteriome formed Gammaproteobacteria (Enterobacteriaceae, Erwiniaceae, Pseudomonadaceae, Moraxellaceae) and then Firmicutes (Streptococcaceae). The diversity and abundance of single ARGs groups were comparable for both samples despite bacteriome differences. More than 50% of the detected ARGs alignments were mutations conferring resistance to aminoglycosides (16S rRNA), resistance to fluoroquinolones (gyrA, gyrB, parC, parD) and elfamycin (EF-Tu). ARGs encoding efflux pumps formed more than 30% of the detected alignments. Beta-lactamases were represented by many variants, but were less abundant.
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Affiliation(s)
- Milada Solcova
- Correspondence: (M.S.); (S.P.); Tel.: +420-220-44-5196 (M.S. & S.P.)
| | | | - Sabina Purkrtova
- Correspondence: (M.S.); (S.P.); Tel.: +420-220-44-5196 (M.S. & S.P.)
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14
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Petruschke H, Schori C, Canzler S, Riesbeck S, Poehlein A, Daniel R, Frei D, Segessemann T, Zimmerman J, Marinos G, Kaleta C, Jehmlich N, Ahrens CH, von Bergen M. Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome. MICROBIOME 2021; 9:55. [PMID: 33622394 PMCID: PMC7903761 DOI: 10.1186/s40168-020-00981-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/16/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. RESULTS We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. CONCLUSIONS We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract. Video abstract.
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Affiliation(s)
- Hannes Petruschke
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Christian Schori
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Sebastian Canzler
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Sarah Riesbeck
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Anja Poehlein
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August University of Göttingen, Göttingen, Germany
| | - Daniel Frei
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Tina Segessemann
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Johannes Zimmerman
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Georgios Marinos
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland.
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany.
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany.
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15
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Lakshmanan R, Kalaimurugan D, Sivasankar P, Arokiyaraj S, Venkatesan S. Identification and characterization of Pseudomonas aeruginosa derived bacteriocin for industrial applications. Int J Biol Macromol 2020; 165:2412-2418. [PMID: 33132130 DOI: 10.1016/j.ijbiomac.2020.10.126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 11/19/2022]
Abstract
Drug resistance has become a major threat due to the frequent use of commercial antibiotics and there is an urgent need to combat this problem. Having this in mind, the present research was aimed at developing a novel P. aeruginosa puBac bacteriocin molecule. The bacteriocin was purified by ammonium sulfate precipitation followed by Sepharose FF and Sephadex G15 column purification and the purified bacteriocin has been reported to have the molar mass of 43 kDa. The findings of the optimization showed that 3500 AU/mL of bacteriocin was obtained at 37 °C, 3410 AU/mL of bacteriocin at 6.5 pH and 3780 AU/mL of bacteriocin at 48 h of incubation time. In addition, 3863 AU/mL of bacteriocin activity was obtained with Tween-80 followed by 3789 AU/mL with a concentration of 2% NaCl and 4200 AU/mL for Fe2+. PuBac bacteriocin has been shown to have a significant effect on test pathogens. For example, E. coli was found to have 3.6 μM of MIC, followed by Staphylococcus sp. with 6.15 μM of MIC and Bacillus sp. with a 7.5 μM of MIC. The remarkable properties of bacteriocin suggest that it could be used in various pharmaceutical and food industries.
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Affiliation(s)
- Ramasamy Lakshmanan
- Department of Environmental Science, School of Life Sciences, Periyar University, Salem 636011, Tamil Nadu, India
| | - Dharman Kalaimurugan
- Department of Environmental Science, School of Life Sciences, Periyar University, Salem 636011, Tamil Nadu, India
| | - Palaniappan Sivasankar
- Department of Environmental Science, School of Life Sciences, Periyar University, Salem 636011, Tamil Nadu, India
| | - Selvaraj Arokiyaraj
- Department of Food Science and Biotechnology, Sejong University, Republic of Korea
| | - Srinivasan Venkatesan
- Department of Environmental Science, School of Life Sciences, Periyar University, Salem 636011, Tamil Nadu, India.
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16
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Bukvicki D, Siroli L, D’Alessandro M, Cosentino S, Fliss I, Said LB, Hassan H, Lanciotti R, Patrignani F. Unravelling the Potential of Lactococcus lactis Strains to Be Used in Cheesemaking Production as Biocontrol Agents. Foods 2020; 9:foods9121815. [PMID: 33297482 PMCID: PMC7762361 DOI: 10.3390/foods9121815] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023] Open
Abstract
This research, developed within an exchange program between Italy and Canada, represents the first step of a three-year project intended to evaluate the potential of nisin-producing Lactococcus lactis strains isolated from Italian and Canadian dairy products to select a consortium of strains to be used as biocontrol agents in Crescenza and Cheddar cheese production. In this framework, the acidification and the production of nisin in milk, and the volatile molecule profiles of the fermented milk, were recorded. The strains were further tested for their anti-Listeria monocytogenes activity in milk. The data obtained highlighted good potential for some of the tested strains, which showed production of nisin beginning within 12 h after the inoculation and reaching maximum levels between 24 and 48 h. The highest inactivation levels of L. monocytogenes in milk was reached in the presence of the strains 101877/1, LBG2, 9FS16, 11FS16, 3LC39, FBG1P, UL36, UL720, UL35. The strains generated in milk-specific volatile profiles and differences in the presence of fundamental aromatic molecules of dairy products, such as 2-butanone and diacetyl. The results highlight the interesting potential of some L. lactis strains, the producer of nisin, to be further used as biocontrol agents, although the strains need to be tested for interaction with traditional thermophilic starters and tested in real cheesemaking conditions.
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Affiliation(s)
- Danka Bukvicki
- Department of Morphology and Systematics of Plants, Faculty of Biology, Institute of Botany and Botanical Garden “Jevremovac”, University of Belgrade, Takovska 43, 11000 Belgrade, Serbia;
| | - Lorenzo Siroli
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (M.D.); (R.L.)
- Interdepartmental Center for Industrial Agri-Food Research, University of Bologna, Piazza Goidanich 60, 47521 Cesena (FC), Italy
| | - Margherita D’Alessandro
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (M.D.); (R.L.)
| | - Sofia Cosentino
- Department of Medical Sciences and Public Health, University of Cagliari, 09042 Monserrato, Italy; (S.C.); (H.H.)
| | - Ismail Fliss
- Food Science Department, Food and Agriculture Faculty, Institute of Nutrition and Functional Foods, Laval University, 2425 Agriculture Street, Quebec City, QC G1V0A6, Canada; (I.F.); (L.B.S.)
| | - Laila Ben Said
- Food Science Department, Food and Agriculture Faculty, Institute of Nutrition and Functional Foods, Laval University, 2425 Agriculture Street, Quebec City, QC G1V0A6, Canada; (I.F.); (L.B.S.)
| | - Hebatoallah Hassan
- Department of Medical Sciences and Public Health, University of Cagliari, 09042 Monserrato, Italy; (S.C.); (H.H.)
| | - Rosalba Lanciotti
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (M.D.); (R.L.)
- Interdepartmental Center for Industrial Agri-Food Research, University of Bologna, Piazza Goidanich 60, 47521 Cesena (FC), Italy
| | - Francesca Patrignani
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (M.D.); (R.L.)
- Interdepartmental Center for Industrial Agri-Food Research, University of Bologna, Piazza Goidanich 60, 47521 Cesena (FC), Italy
- Correspondence: ; Tel.: +39-0547-338133
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17
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Schlei KP, Angioletti BL, Fernandes de Carvalho L, Bertoli SL, Ratto Reiter MG, Krebs de Souza C. Influence of temperature on microbial growth during processing of kochkäse cheese made from raw and pasteurised milk. Int Dairy J 2020. [DOI: 10.1016/j.idairyj.2020.104786] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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In Vitro Evaluation of Potential Probiotic Strain Lactococcus lactis Gh1 and Its Bacteriocin-Like Inhibitory Substances for Potential Use in the Food Industry. Probiotics Antimicrob Proteins 2020; 13:422-440. [PMID: 32728855 DOI: 10.1007/s12602-020-09690-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Determination of a microbial strain for the joining into sustenance items requires both in vitro and in vivo assessment. A newly isolated bacteriocin-like inhibitory substance (BLIS) producing lactic acid bacterium, Lactococcus lactis Gh1, was isolated from a traditional flavour enhancer and evaluated in vitro for its potential applications in the food industry. Results from this study showed that L. lactis was tolerant to NaCl (≤ 4.0%, w/v), phenol (≤ 0.4%, w/v), 0.3% (w/v) bile salt, and pH 3. BLIS from L. lactis showed antimicrobial activity against Listeria monocytogenes ATCC 15313 and was susceptible to 10 types of antibiotics. The absence of haemolytic activity and the presence of acid phosphatase and naphthol-AS-BI-phosphohydrolase were observed in L. lactis. L. lactis could coagulate milk and showed a negative response to amylolytic and proteolytic activities and did not secrete β-galactosidase. The antimicrobial activity of BLIS was completely abolished at 121 °C. The BLIS was conserved at 4 °C in BHI and MRS medium up to 6-4 months, respectively. BLIS activity was more stable in BHI as compared to MRS after four freeze-thaw cycles and was not affected by a wide range of pH (pH 4-8). BLIS was sensitive to proteinase k and resistant to catalase and trypsin. The antimicrobial activity was slightly reduced by acetone, ethanol, methanol, and acetonitrile at 10% (v/v) and also towards Tween-80, urea, and NaCl 1% (v/v). Results from this study have demonstrated that L. lactis has a vast potential to be applied in the food industry, such as for the preparation of starter culture, functional foods, and probiotic products.
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19
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Kim SW, Ha YJ, Bang KH, Lee S, Yeo JH, Yang HS, Kim TW, Lee KP, Bang WY. Potential of Bacteriocins from Lactobacillus taiwanensis for Producing Bacterial Ghosts as a Next Generation Vaccine. Toxins (Basel) 2020; 12:toxins12070432. [PMID: 32630253 PMCID: PMC7404994 DOI: 10.3390/toxins12070432] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/18/2020] [Accepted: 06/28/2020] [Indexed: 12/22/2022] Open
Abstract
Bacteriocins are functionally diverse toxins produced by most microbes and are potent antimicrobial peptides (AMPs) for bacterial ghosts as next generation vaccines. Here, we first report that the AMPs secreted from Lactobacillus taiwanensis effectively form ghosts of pathogenic bacteria and are identified as diverse bacteriocins, including novel ones. In detail, a cell-free supernatant from L. taiwanensis exhibited antimicrobial activities against pathogenic bacteria and was observed to effectively cause cellular lysis through pore formation in the bacterial membrane using scanning electron microscopy (SEM). The treatment of the cell-free supernatant with proteinase K or EDTA proved that the antimicrobial activity is mediated by AMPs, and the purification of AMPs using Sep-Pak columns indicated that the cell-free supernatant includes various amphipathic peptides responsible for the antimicrobial activity. Furthermore, the whole-genome sequencing of L. taiwanensis revealed that the strain has diverse bacteriocins, confirmed experimentally to function as AMPs, and among them are three novel bacteriocins, designated as Tan 1, Tan 2, and Tan 3. We also confirmed, using SEM, that Tan 2 effectively produces bacterial ghosts. Therefore, our data suggest that the bacteriocins from L. taiwanensis are potentially useful as a critical component for the preparation of bacterial ghosts.
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Affiliation(s)
- Sam Woong Kim
- Gene Analysis Center, Gyeongnam National University of Science & Technology, Jinju 52725, Korea;
| | - Yeon Jo Ha
- Department of Pharmaceutical Engineering, Gyeongnam National University of Science and Technology, Jinju 52725, Korea; (Y.J.H.); (K.H.B.)
| | - Kyu Ho Bang
- Department of Pharmaceutical Engineering, Gyeongnam National University of Science and Technology, Jinju 52725, Korea; (Y.J.H.); (K.H.B.)
| | - Seungki Lee
- National Institute of Biological Resources (NIBR), Environmental Research Complex, Incheon 22689, Korea; (S.L.); (J.-H.Y.); (H.-S.Y.)
| | - Joo-Hong Yeo
- National Institute of Biological Resources (NIBR), Environmental Research Complex, Incheon 22689, Korea; (S.L.); (J.-H.Y.); (H.-S.Y.)
| | - Hee-Sun Yang
- National Institute of Biological Resources (NIBR), Environmental Research Complex, Incheon 22689, Korea; (S.L.); (J.-H.Y.); (H.-S.Y.)
| | - Tae-Won Kim
- Department of pharmacology, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Korea;
| | - Kyu Pil Lee
- Department of physiology, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Korea
- Correspondence: (K.P.L.); (W.Y.B.); Tel.: +82-42-821-6754 (K.P.L.); +82-32-590-7206 (W.Y.B.)
| | - Woo Young Bang
- National Institute of Biological Resources (NIBR), Environmental Research Complex, Incheon 22689, Korea; (S.L.); (J.-H.Y.); (H.-S.Y.)
- Correspondence: (K.P.L.); (W.Y.B.); Tel.: +82-42-821-6754 (K.P.L.); +82-32-590-7206 (W.Y.B.)
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20
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Papizadeh M, Rohani M, Hosseini SN, Shojaosadati SA, Nahrevanian H, Talebi M, Pourshafie MR. Screening for efficient nitrogen sources for overproduction of the biomass of the functionally probiotic L. plantarum strain RPR42 in a cane molasses-based medium. AMB Express 2020; 10:53. [PMID: 32185601 PMCID: PMC7078425 DOI: 10.1186/s13568-020-00976-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 02/26/2020] [Indexed: 11/10/2022] Open
Abstract
Nitrogen source has a vital role for the efficient growth of lactobacilli. The effects of cheese whey, corn steep liquor, and wheat germ extract on the growth of L. plantarum strain RPR42 in cane molasses-based media was evaluated using various approaches of design of experiments. Our results showed that such protein-rich agricultural by-products significantly increase the biomass production of the strain RPR42 in cane molasses-based media. The most affecting nitrogenous material was cheese whey followed by CSL and the minor effect was reported for wheat germ extract as revealed in factorial and Box–Behnken design experiments. The replacement of costly beef extract and yeast extract with a defined mixtures of the above nitrogenous agricultural by-products in cane molasses-based medium led to production of up to 12.64 g/L/24 h of dry biomass of strain RPR42. A detectable cell density of strain RPR42 (~ 9.81 × 109 CFU/mL 24 h) which was observed in such an economic medium showed that the large-scale production of the strain RPR42 tend to be feasible at significantly low costs.
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