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Sugrue I, Ross RP, Hill C. Bacteriocin diversity, function, discovery and application as antimicrobials. Nat Rev Microbiol 2024:10.1038/s41579-024-01045-x. [PMID: 38730101 DOI: 10.1038/s41579-024-01045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2024] [Indexed: 05/12/2024]
Abstract
Bacteriocins are potent antimicrobial peptides that are produced by bacteria. Since their discovery almost a century ago, diverse peptides have been discovered and described, and some are currently used as commercial food preservatives. Many bacteriocins exhibit extensively post-translationally modified structures encoded on complex gene clusters, whereas others have simple linear structures. The molecular structures, mechanisms of action and resistance have been determined for a number of bacteriocins, but most remain incompletely characterized. These gene-encoded peptides are amenable to bioengineering strategies and heterologous expression, enabling metagenomic mining and modification of novel antimicrobials. The ongoing global antimicrobial resistance crisis demands that novel therapeutics be developed to combat infectious pathogens. New compounds that are target-specific and compatible with the resident microbiota would be valuable alternatives to current antimicrobials. As bacteriocins can be broad or narrow spectrum in nature, they are promising tools for this purpose. However, few bacteriocins have gone beyond preclinical trials and none is currently used therapeutically in humans. In this Review, we explore the broad diversity in bacteriocin structure and function, describe identification and optimization methods and discuss the reasons behind the lack of translation beyond the laboratory of these potentially valuable antimicrobials.
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Affiliation(s)
- Ivan Sugrue
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
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Huang YC, Khumsupan D, Lin SP, Santoso SP, Hsu HY, Cheng KC. Production of bacterial cellulose (BC)/nisin composite with enhanced antibacterial and mechanical properties through co-cultivation of Komagataeibacter xylinum and Lactococcus lactis subsp. lactis. Int J Biol Macromol 2024; 258:128977. [PMID: 38154722 DOI: 10.1016/j.ijbiomac.2023.128977] [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: 09/23/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
By employing co-cultivation technique on Komagataeibacter xylinum and Lactococcus lactis subsp. lactis, bacterial cellulose (BC)/nisin films with improved antibacterial activity and mechanical properties were successfully produced. The findings demonstrated that increased nisin production is associated with an upregulation of gene expression. Furthermore, results from Scanning electronic microscopy (SEM), Fourier transform infrared (FTIR), X-ray diffraction (XRD), and Thermogravimetric analysis (TG) confirmed the integration of nisin within BC. While being biocompatible with human cells, the BC/nisin composites exhibited antimicrobial activity. Moreover, mechanical property analyses showed a noticeable improvement in Young's modulus, tensile strength, and elongation at break by 161, 271, and 195 %, respectively. Additionally, the nisin content in fermentation broth was improved by 170 % after co-culture, accompanied by an 8 % increase in pH as well as 10 % decrease in lactate concentration. Real-time reverse transcription PCR analysis revealed an upregulation of 11 nisin-related genes after co-cultivation, with the highest increase in nisA (5.76-fold). To our knowledge, this is the first study which demonstrates that an increase in secondary metabolites after co-culturing is modulated by gene expression. This research offers a cost-effective approach for BC composite production and presents a technique to enhance metabolite concentration through the regulation of relevant genes.
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Affiliation(s)
- Yi-Cheng Huang
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Darin Khumsupan
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Shin-Ping Lin
- School of Food Safety, Taipei Medical University, Taipei City 110, Taiwan
| | - Shella Permatasari Santoso
- Department of Chemical Engineering, Widya Mandala Surabaya Catholic University, Kalijudan 37, Surabaya 60114, Indonesia; Collaborative Research Center for Sustainable and Zero Waste Industries, Kalijudan 37, Surabaya 60114, East Java, Indonesia
| | - Hsien-Yi Hsu
- Department of Materials Science and Engineering, School of Energy and Environment, City University of Hong Kong, 999077, Hong Kong; Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| | - Kuan-Chen Cheng
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan; Institute of Food Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan; Department of Optometry, Asia University, 500, Lioufeng Rd., Wufeng, Taichung, Taiwan 41354; Department of Medical Research, China Medical University Hospital, China Medical University, 91, Hsueh-Shih Road, Taichung 40402, Taiwan.
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Karlsen ST, Rau MH, Sánchez BJ, Jensen K, Zeidan AA. From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry. FEMS Microbiol Rev 2023; 47:fuad030. [PMID: 37286882 PMCID: PMC10337747 DOI: 10.1093/femsre/fuad030] [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: 02/28/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/09/2023] Open
Abstract
When selecting microbial strains for the production of fermented foods, various microbial phenotypes need to be taken into account to achieve target product characteristics, such as biosafety, flavor, texture, and health-promoting effects. Through continuous advances in sequencing technologies, microbial whole-genome sequences of increasing quality can now be obtained both cheaper and faster, which increases the relevance of genome-based characterization of microbial phenotypes. Prediction of microbial phenotypes from genome sequences makes it possible to quickly screen large strain collections in silico to identify candidates with desirable traits. Several microbial phenotypes relevant to the production of fermented foods can be predicted using knowledge-based approaches, leveraging our existing understanding of the genetic and molecular mechanisms underlying those phenotypes. In the absence of this knowledge, data-driven approaches can be applied to estimate genotype-phenotype relationships based on large experimental datasets. Here, we review computational methods that implement knowledge- and data-driven approaches for phenotype prediction, as well as methods that combine elements from both approaches. Furthermore, we provide examples of how these methods have been applied in industrial biotechnology, with special focus on the fermented food industry.
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Affiliation(s)
- Signe T Karlsen
- Bioinformatics & Modeling, R&D Digital Innovation, Chr. Hansen A/S, Bøge Allé 10-12, 2970 Hørsholm, Denmark
| | - Martin H Rau
- Bioinformatics & Modeling, R&D Digital Innovation, Chr. Hansen A/S, Bøge Allé 10-12, 2970 Hørsholm, Denmark
| | - Benjamín J Sánchez
- Bioinformatics & Modeling, R&D Digital Innovation, Chr. Hansen A/S, Bøge Allé 10-12, 2970 Hørsholm, Denmark
| | - Kristian Jensen
- Bioinformatics & Modeling, R&D Digital Innovation, Chr. Hansen A/S, Bøge Allé 10-12, 2970 Hørsholm, Denmark
| | - Ahmad A Zeidan
- Bioinformatics & Modeling, R&D Digital Innovation, Chr. Hansen A/S, Bøge Allé 10-12, 2970 Hørsholm, Denmark
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Field D, Fernandez de Ullivarri M, Ross RP, Hill C. After a century of nisin research - where are we now? FEMS Microbiol Rev 2023; 47:fuad023. [PMID: 37300874 PMCID: PMC10257480 DOI: 10.1093/femsre/fuad023] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/13/2023] Open
Abstract
It is almost a century since nisin was discovered in fermented milk cultures, coincidentally in the same year that penicillin was first described. Over the last 100 years this small, highly modified pentacyclic peptide has not only found success in the food industry as a preservative but has also served as the paradigm for our understanding of the genetic organization, expression, and regulation of genes involved in lantibiotic biosynthesis-one of the few cases of extensive post-translation modification in prokaryotes. Recent developments in understanding the complex biosynthesis of nisin have shed light on the cellular location of the modification and transport machinery and the co-ordinated series of spatio-temporal events required to produce active nisin and provide resistance and immunity. The continued unearthing of new natural variants from within human and animal gastrointestinal tracts has sparked interest in the potential application of nisin to influence the microbiome, given the growing recognition of the role the gastrointestinal microbiota plays in health and disease. Moreover, interdisciplinary approaches have taken advantage of biotechnological advancements to bioengineer nisin to produce novel variants and expand nisin functionality for applications in the biomedical field. This review will discuss the latest progress in these aspects of nisin research.
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Affiliation(s)
- Des Field
- APC Microbiome Ireland, University College Cork,Western Road, Cork T12 YN60, Ireland
- School of Microbiology, University College Cork, College Road, Cork T12 YT20, Ireland
| | | | - R Paul Ross
- APC Microbiome Ireland, University College Cork,Western Road, Cork T12 YN60, Ireland
- School of Microbiology, University College Cork, College Road, Cork T12 YT20, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork,Western Road, Cork T12 YN60, Ireland
- School of Microbiology, University College Cork, College Road, Cork T12 YT20, Ireland
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Nisin E Is a Novel Nisin Variant Produced by Multiple Streptococcus equinus Strains. Microorganisms 2023; 11:microorganisms11020427. [PMID: 36838392 PMCID: PMC9958725 DOI: 10.3390/microorganisms11020427] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/23/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Nisin A, the prototypical lantibiotic, is an antimicrobial peptide currently utilised as a food preservative, with potential for therapeutic applications. Here, we describe nisin E, a novel nisin variant produced by two Streptococcus equinus strains, APC4007 and APC4008, isolated from sheep milk. Shotgun whole genome sequencing and analysis revealed biosynthetic gene clusters similar to nisin U, with a unique rearrangement of the core peptide encoding gene within the cluster. The 3100.8 Da peptide by MALDI-TOF mass spectrometry, is 75% identical to nisin A, with 10 differences, including 2 deletions: Ser29 and Ile30, and 8 substitutions: Ile4Lys, Gly18Thr, Asn20Pro, Met21Ile, His27Gly, Val32Phe, Ser33Gly, and Lys34Asn. Nisin E producing strains inhibited species of Lactobacillus, Bacillus, and Clostridiodes and were immune to nisin U. Sequence alignment identified putative promoter sequences across the nisin producer genera, allowing for the prediction of genes in Streptococcus to be potentially regulated by nisin. S. equinus pangenome BLAST analyses detected 6 nisin E operons across 44 publicly available genomes. An additional 20 genomes contained a subset of nisin E transport/immunity and regulatory genes (nseFEGRK), without adjacent peptide production genes. These genes suggest that nisin E response mechanisms, distinct from the canonical nisin immunity and resistance operons, are widespread across the S. equinus species. The discovery of this new nisin variant and its immunity determinants in S. equinus suggests a central role for nisin in the competitive nature of the species.
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Bourdichon F, Arias E, Babuchowski A, Bückle A, Bello FD, Dubois A, Fontana A, Fritz D, Kemperman R, Laulund S, McAuliffe O, Miks MH, Papademas P, Patrone V, Sharma DK, Sliwinski E, Stanton C, Von Ah U, Yao S, Morelli L. The forgotten role of food cultures. FEMS Microbiol Lett 2021; 368:fnab085. [PMID: 34223876 PMCID: PMC8397475 DOI: 10.1093/femsle/fnab085] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 07/01/2021] [Indexed: 12/15/2022] Open
Abstract
Fermentation is one of if not the oldest food processing technique, yet it is still an emerging field when it comes to its numerous mechanisms of action and potential applications. The effect of microbial activity on the taste, bioavailability and preservation of the nutrients and the different food matrices has been deciphered by the insights of molecular microbiology. Among those roles of fermentation in the food chain, biopreservation remains the one most debated. Presumably because it has been underestimated for quite a while, and only considered - based on a food safety and technological approach - from the toxicological and chemical perspective. Biopreservation is not considered as a traditional use, where it has been by design - but forgotten - as the initial goal of fermentation. The 'modern' use of biopreservation is also slightly different from the traditional use, due mainly to changes in cooling of food and other ways of preservation, Extending shelf life is considered to be one of the properties of food additives, classifying - from our perspective - biopreservation wrongly and forgetting the role of fermentation and food cultures. The present review will summarize the current approaches of fermentation as a way to preserve and protect the food, considering the different way in which food cultures and this application could help tackle food waste as an additional control measure to ensure the safety of the food.
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Affiliation(s)
- François Bourdichon
- Food Safety, Microbiology, Hygiene, 16 Rue Gaston de Caillavet, 75015 Paris, France
- Facoltà di Scienze agrarie, alimentarie ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense, Piacenza-Cremona, Italy
| | - Emmanuelle Arias
- AGROSCOPE, Food Microbial Systems, Schwarzenburgstrasse 161, CH-3003 Bern, Switzerland
| | | | - Anne Bückle
- Milchprüfring Baden-Württemberg e.V., Marie-Curie-Straße 19, 73230 Kirchheim, u.T., Germany
| | | | - Aurélie Dubois
- International Dairy Federationiry Federation, 70 Boulevard Auguste Reyers, 1030 Brussels, Belgium
| | - Alessandra Fontana
- Facoltà di Scienze agrarie, alimentarie ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense, Piacenza-Cremona, Italy
| | - Duresa Fritz
- International Flavors and Fragrances, 20 rue Brunel, Paris 75017, France
| | - Rober Kemperman
- Lesaffre International, 152 rue du Docteur Yersin, 59120 Loos, France
| | - Svend Laulund
- Chr. Hansen A/S, Agern Allé 24, 2970 Hoersholm, Denmark
| | | | - Marta Hanna Miks
- Glycom A/S, Kogle Allé 4, 2970 Hørsholm, Denmark
- Faculty of Food Science, Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszynski 1, 10–726 Olsztyn, Poland
| | - Photis Papademas
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Archiepiskopou Kyprianou, PO BOX 50329, Limassol, Cyprus
| | - Vania Patrone
- Facoltà di Scienze agrarie, alimentarie ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense, Piacenza-Cremona, Italy
| | | | - Edward Sliwinski
- The European Federation of Food Science & Technology, Nieuwe Kanaal 9a, 6709 PA, Wageningen, The Netherlands
| | | | - Ueli Von Ah
- AGROSCOPE, Food Microbial Systems, Schwarzenburgstrasse 161, CH-3003 Bern, Switzerland
| | - Su Yao
- China National Research Institute of Food & Fermentation Industries, China Center of Industrial Culture Collection, Building 6, No.24, Jiuxianqiaozhong Road, Chaoyang District, Beijing 100015, PR China
| | - Lorenzo Morelli
- Facoltà di Scienze agrarie, alimentarie ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense, Piacenza-Cremona, Italy
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