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Jansen van Rensburg MJ, Berger DJ, Yassine I, Shaw D, Fohrmann A, Bray JE, Jolley KA, Maiden MCJ, Brueggemann AB. Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure. Microb Genom 2024; 10:001280. [PMID: 39137139 PMCID: PMC11321556 DOI: 10.1099/mgen.0.001280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 07/17/2024] [Indexed: 08/15/2024] Open
Abstract
Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonization, disease, antimicrobial resistance and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enhances the development of robust genome-wide typing schemes to define the overall bacterial population structure and lineages within it. Using the previously published data, we developed the Pneumococcal Genome Library (PGL), a curated dataset of 30 976 genomes and contextual data for carriage and disease pneumococci recovered between 1916 and 2018 in 82 countries. We leveraged the size and diversity of the PGL to develop a core genome multilocus sequence typing (cgMLST) scheme comprised of 1222 loci. Finally, using multilevel single-linkage clustering, we stratified pneumococci into hierarchical clusters based on allelic similarity thresholds and defined these with a taxonomic life identification number (LIN) barcoding system. The PGL, cgMLST scheme and LIN barcodes represent a high-quality genomic resource and fine-scale clustering approaches for the analysis of pneumococcal populations, which support the genomic epidemiology and surveillance of this leading global pathogen.
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Affiliation(s)
| | - Duncan J. Berger
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Iman Yassine
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - David Shaw
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Andy Fohrmann
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - James E. Bray
- Department of Biology, University of Oxford, Oxford, UK
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2
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Butler MEB, Jansen van Rensburg MJ, Karani A, Mvera B, Akech D, Akter A, Forrest C, van Tonder AJ, Quirk SJ, Haraldsson G, Bentley SD, Erlendsdóttir H, Haraldsson Á, Kristinsson KG, Scott JAG, Brueggemann AB. Nasopharyngeal competition dynamics are likely to be altered following vaccine introduction: bacteriocin prevalence and diversity among Icelandic and Kenyan pneumococci. Microb Genom 2023; 9:mgen001060. [PMID: 37436819 PMCID: PMC10438807 DOI: 10.1099/mgen.0.001060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/09/2023] [Indexed: 07/13/2023] Open
Abstract
Bacteriocins are antimicrobial peptides produced by bacteria to inhibit other bacteria in the surrounding environment. Streptococcus pneumoniae is a leading cause of disease worldwide and colonises the healthy human nasopharynx, where it competes for space and nutrients. Pneumococcal conjugate vaccines have reduced the incidence of disease, but they also restructure the bacterial population, and this restructuring likely alters the nasopharyngeal competition dynamics. Here, the distribution of bacteriocins was examined in over 5000 carriage and disease-causing pneumococci from Iceland and Kenya, recovered before and after the introduction of pneumococcal vaccination. Overall, up to eleven different bacteriocin gene clusters were identified per pneumococcus. Significant differences in the prevalence of bacteriocins were observed before and after vaccine introduction, and among carriage and disease-causing pneumococci, which were largely explained by the bacterial population structure. Genetically similar pneumococci generally harboured the same bacteriocins although sometimes different repertoires of bacteriocins were observed, which suggested that horizontal transfer of bacteriocin clusters had occurred. These findings demonstrated that vaccine-mediated changes in the pneumococcal population altered the prevalence and distribution of bacteriocins. The consequences of this for pneumococcal colonisation and disease remain to be determined.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Sigríður J. Quirk
- University of Iceland and Landspitali - The National University Hospital of Iceland, Reykjavík, Iceland
| | - Gunnsteinn Haraldsson
- University of Iceland and Landspitali - The National University Hospital of Iceland, Reykjavík, Iceland
| | | | - Helga Erlendsdóttir
- University of Iceland and Landspitali - The National University Hospital of Iceland, Reykjavík, Iceland
| | - Ásgeir Haraldsson
- University of Iceland and Children’s Hospital Iceland, Landspitali, Reykjavík, Iceland
| | - Karl G. Kristinsson
- University of Iceland and Landspitali - The National University Hospital of Iceland, Reykjavík, Iceland
| | - J. Anthony G. Scott
- KEMRI Wellcome Trust Programme, Kilifi, Kenya
- London School of Hygiene and Tropical Medicine, London, UK
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3
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Fischer SW, Titgemeyer F. Protective Cultures in Food Products: From Science to Market. Foods 2023; 12:foods12071541. [PMID: 37048362 PMCID: PMC10094266 DOI: 10.3390/foods12071541] [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: 03/01/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 04/14/2023] Open
Abstract
An ultimate goal in food production is to guarantee food safety and security. Fermented food products benefit from the intrinsic capabilities of the applied starter cultures as they produce organic acids and bactericidal compounds such as hydrogen peroxide that hamper most food pathogens. In addition, highly potent small peptides, bacteriocins, are being expelled to exert antibiotic effects. Based on ongoing scientific efforts, there is a growing market of food products to which protective cultures are added exclusively for food safety and for prolonged shelf life. In this regard, most genera from the order Lactobacillales play a prominent role. Here, we give an overview on protective cultures in food products. We summarize the mode of actions of antibacterial mechanisms. We display the strategies for the isolation and characterization of protective cultures in order to have them market-ready. A survey of the growing market reveals promising perspectives. Finally, a comprehensive chapter discusses the current legislation issues concerning protective cultures, leading to the conclusion that the application of protective cultures is superior to the usage of defined bacteriocins regarding simplicity, economic costs, and thus usage in less-developed countries. We believe that further discovery of bacteria to be implemented in food preservation will significantly contribute to customer's food safety and food security, badly needed to feed world's growing population but also for food waste reduction in order to save substantial amounts of greenhouse gas emissions.
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Affiliation(s)
- Sebastian W Fischer
- Department of Food, Nutrition and Facilities, FH Muenster, Correnstr. 25, 48149 Münster, Germany
| | - Fritz Titgemeyer
- Department of Food, Nutrition and Facilities, FH Muenster, Correnstr. 25, 48149 Münster, Germany
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4
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Tagg JR, Harold LK, Jain R, Hale JDF. Beneficial modulation of human health in the oral cavity and beyond using bacteriocin-like inhibitory substance-producing streptococcal probiotics. Front Microbiol 2023; 14:1161155. [PMID: 37056747 PMCID: PMC10086258 DOI: 10.3389/fmicb.2023.1161155] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/03/2023] [Indexed: 03/30/2023] Open
Abstract
The human oral cavity contains a diversity of microbial habitats that have been adopted and adapted to as homeland by an amazingly heterogeneous population of microorganisms collectively referred to as the oral microbiota. These microbes generally co-habit in harmonious homeostasis. However, under conditions of imposed stress, as with changes to the host’s physiology or nutritional status, or as a response to foreign microbial or antimicrobial incursions, some components of the oral “microbiome” (viz. the in situ microbiota) may enter a dysbiotic state. This microbiome dysbiosis can manifest in a variety of guises including streptococcal sore throats, dental caries, oral thrush, halitosis and periodontal disease. Most of the strategies currently available for the management or treatment of microbial diseases of the oral cavity focus on the repetitive “broad sweep” and short-term culling of oral microbe populations, hopefully including the perceived principal pathogens. Both physical and chemical techniques are used. However, the application of more focused approaches to the harnessing or elimination of key oral cavity pathogens is now feasible through the use of probiotic strains that are naturally adapted for oral cavity colonization and also are equipped to produce anti-competitor molecules such as the bacteriocins and bacteriocin-like inhibitory substances (viz BLIS). Some of these probiotics are capable of suppressing the proliferation of a variety of recognized microbial pathogens of the human mouth, thereby assisting with the restoration of oral microbiome homeostasis. BLIS K12 and BLIS M18, the progenitors of the BLIS-producing oral probiotics, are members of the human oral cavity commensal species Streptococcus salivarius. More recently however, a number of other streptococcal and some non-streptococcal candidate oral probiotics have also been promoted. What is becoming increasingly apparent is that the future for oral probiotic applications will probably extend well beyond the attempted limitation of the direct pathological consequences of oral microbiome dysbiosis to also encompass a plethora of systemic diseases and disorders of the human host. The background to and the evolving prospects for the beneficial modulation of the oral microbiome via the application of BLIS-producing S. salivarius probiotics comprises the principal focus of the present review.
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Dijamentiuk A, Mangavel C, Elfassy A, Michaux F, Burgain J, Rondags E, Delaunay S, Ferrigno S, Revol-Junelles AM, Borges F. Invert emulsions alleviate biotic interactions in bacterial mixed culture. Microb Cell Fact 2023; 22:16. [PMID: 36670385 PMCID: PMC9854087 DOI: 10.1186/s12934-022-02014-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/31/2022] [Indexed: 01/21/2023] Open
Abstract
The large application potential of microbiomes has led to a great need for mixed culture methods. However, microbial interactions can compromise the maintenance of biodiversity during cultivation in a reactor. In particular, competition among species can lead to a strong disequilibrium in favor of the fittest microorganism. In this study, an invert emulsion system was designed by dispersing culture medium in a mixture of sunflower oil and the surfactant PGPR. Confocal laser scanning microscopy revealed that this system allowed to segregate microorganisms in independent droplets. Granulomorphometric analysis showed that the invert emulsion remains stable during at least 24 h, and that the introduction of bacteria did not have a significant impact on the structure of the invert emulsion. A two-strain antagonistic model demonstrated that this invert emulsion system allows the propagation of two strains without the exclusion of the less-fit bacterium. The monitoring of single-strain cultures of bacteria representative of a cheese microbiota revealed that all but Brevibacterium linens were able to grow. A consortium consisting of Lactococcus lactis subsp. lactis biovar diacetylactis, Streptococcus thermophilus, Leuconostoc mesenteroides, Staphylococcus xylosus, Lactiplantibacillus plantarum and Carnobacterium maltaromaticum was successfully cultivated without detectable biotic interactions. Metabarcoding analysis revealed that the system allowed a better maintenance of alpha diversity and produced a propagated bacterial consortium characterized by a structure closer to the initial state compared to non-emulsified medium. This culture system could be an important tool in the field of microbial community engineering.
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Affiliation(s)
- Alexis Dijamentiuk
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Cécile Mangavel
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Annelore Elfassy
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Florentin Michaux
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Jennifer Burgain
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Emmanuel Rondags
- grid.29172.3f0000 0001 2194 6418LRGP, Université de Lorraine, Nancy, France
| | - Stéphane Delaunay
- grid.29172.3f0000 0001 2194 6418LRGP, Université de Lorraine, Nancy, France
| | - Sandie Ferrigno
- grid.29172.3f0000 0001 2194 6418IECL, Equipe BIGS, INRIA Nancy, Université de Lorraine, Nancy, France
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6
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Aggarwal SD, Lees JA, Jacobs NT, Bee GCW, Abruzzo AR, Weiser JN. BlpC-mediated selfish program leads to rapid loss of Streptococcus pneumoniae clonal diversity during infection. Cell Host Microbe 2023; 31:124-134.e5. [PMID: 36395758 PMCID: PMC9839470 DOI: 10.1016/j.chom.2022.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/27/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022]
Abstract
Successful colonization of a host requires bacterial adaptation through genetic and population changes that are incompletely defined. Using chromosomal barcoding and high-throughput sequencing, we investigate the population dynamics of Streptococcus pneumoniae during infant mouse colonization. Within 1 day post inoculation, diversity was reduced >35-fold with expansion of a single clonal lineage. This loss of diversity was not due to immune factors, microbiota, or exclusive genetic drift. Rather, bacteriocins induced by the BlpC-quorum sensing pheromone resulted in predation of kin cells. In this intra-strain competition, the subpopulation reaching a quorum likely eliminates others that have yet to activate the blp locus. Additionally, this reduced diversity restricts the number of unique clones that establish colonization during transmission between hosts. Genetic variation in the blp locus was also associated with altered transmissibility in a human population, further underscoring the importance of BlpC in clonal selection and its role as a selfish element.
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Affiliation(s)
- Surya D Aggarwal
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA.
| | - John A Lees
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA; European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton CB10 1SD, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W12 7TA, UK
| | - Nathan T Jacobs
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Gavyn Chern Wei Bee
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Annie R Abruzzo
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jeffrey N Weiser
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA.
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7
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Oyama LB, Olleik H, Teixeira ACN, Guidini MM, Pickup JA, Hui BYP, Vidal N, Cookson AR, Vallin H, Wilkinson T, Bazzolli DMS, Richards J, Wootton M, Mikut R, Hilpert K, Maresca M, Perrier J, Hess M, Mantovani HC, Fernandez-Fuentes N, Creevey CJ, Huws SA. In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus. NPJ Biofilms Microbiomes 2022; 8:58. [PMID: 35835775 PMCID: PMC9283466 DOI: 10.1038/s41522-022-00320-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 06/21/2022] [Indexed: 12/29/2022] Open
Abstract
Here we report two antimicrobial peptides (AMPs), HG2 and HG4 identified from a rumen microbiome metagenomic dataset, with activity against multidrug-resistant (MDR) bacteria, especially methicillin-resistant Staphylococcus aureus (MRSA) strains, a major hospital and community-acquired pathogen. We employed the classifier model design to analyse, visualise, and interpret AMP activities. This approach allowed in silico discrimination of promising lead AMP candidates for experimental evaluation. The lead AMPs, HG2 and HG4, are fast-acting and show anti-biofilm and anti-inflammatory activities in vitro and demonstrated little toxicity to human primary cell lines. The peptides were effective in vivo within a Galleria mellonella model of MRSA USA300 infection. In terms of mechanism of action, HG2 and HG4 appear to interact with the cytoplasmic membrane of target cells and may inhibit other cellular processes, whilst preferentially binding to bacterial lipids over human cell lipids. Therefore, these AMPs may offer additional therapeutic templates for MDR bacterial infections.
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Affiliation(s)
- Linda B. Oyama
- grid.4777.30000 0004 0374 7521Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland BT9 5DL UK
| | - Hamza Olleik
- grid.6227.10000000121892165CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Sorbonne Universités, Rue du Docteur Schweitzer, CS 60319, CEDEX, 60203 Compiègne, France
| | - Ana Carolina Nery Teixeira
- grid.12799.340000 0000 8338 6359Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, 36570-900 Brasil
| | - Matheus M. Guidini
- grid.12799.340000 0000 8338 6359Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, 36570-900 Brasil
| | - James A. Pickup
- grid.4777.30000 0004 0374 7521Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland BT9 5DL UK
| | - Brandon Yeo Pei Hui
- University College Fairview (UCF), 4178, Jalan 1/27D, Section 6, Wangsa Maju, 53300 Kuala Lumpur, Malaysia
| | - Nicolas Vidal
- grid.5399.60000 0001 2176 4817Yelen Analytics, Aix-Marseille University ICR, 13013 Marseille, France
| | - Alan R. Cookson
- grid.8186.70000 0001 2168 2483Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales SY23 3DA UK
| | - Hannah Vallin
- grid.8186.70000 0001 2168 2483Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales SY23 3DA UK
| | - Toby Wilkinson
- grid.4305.20000 0004 1936 7988The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
| | - Denise M. S. Bazzolli
- grid.12799.340000 0000 8338 6359Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, 36570-900 Brasil
| | - Jennifer Richards
- grid.241103.50000 0001 0169 7725Specialist Antimicrobial Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW UK
| | - Mandy Wootton
- grid.241103.50000 0001 0169 7725Specialist Antimicrobial Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW UK
| | - Ralf Mikut
- grid.7892.40000 0001 0075 5874Karlsruhe Institute of Technology, Institute for Automation and Applied Informatics, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein, Leopoldshafen Germany
| | - Kai Hilpert
- grid.4464.20000 0001 2161 2573Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London, SW17 0RE UK
| | - Marc Maresca
- grid.5399.60000 0001 2176 4817Aix Marseille University, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Josette Perrier
- grid.5399.60000 0001 2176 4817Aix Marseille University, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Matthias Hess
- grid.27860.3b0000 0004 1936 9684UC Davis, College of Agricultural and Environmental Sciences, California, 95616 CA USA
| | - Hilario C. Mantovani
- grid.12799.340000 0000 8338 6359Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, 36570-900 Brasil
| | - Narcis Fernandez-Fuentes
- grid.8186.70000 0001 2168 2483Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales SY23 3DA UK
| | - Christopher J. Creevey
- grid.4777.30000 0004 0374 7521Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland BT9 5DL UK
| | - Sharon A. Huws
- grid.4777.30000 0004 0374 7521Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland BT9 5DL UK
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Biogeography of Bacterial Communities and Specialized Metabolism in Human Aerodigestive Tract Microbiomes. Microbiol Spectr 2021; 9:e0166921. [PMID: 34704787 PMCID: PMC8549736 DOI: 10.1128/spectrum.01669-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The aerodigestive tract (ADT) is the primary portal through which pathogens and other invading microbes enter the body. As the direct interface with the environment, we hypothesize that the ADT microbiota possess biosynthetic gene clusters (BGCs) for antibiotics and other specialized metabolites to compete with both endogenous and exogenous microbes. From 1,214 bacterial genomes, representing 136 genera and 387 species that colonize the ADT, we identified 3,895 BGCs. To determine the distribution of BGCs and bacteria in different ADT sites, we aligned 1,424 metagenomes, from nine different ADT sites, onto the predicted BGCs. We show that alpha diversity varies across the ADT and that each site is associated with distinct bacterial communities and BGCs. We identify specific BGC families enriched in the buccal mucosa, external naris, gingiva, and tongue dorsum despite these sites harboring closely related bacteria. We reveal BGC enrichment patterns indicative of the ecology at each site. For instance, aryl polyene and resorcinol BGCs are enriched in the gingiva and tongue, which are colonized by many anaerobes. In addition, we find that streptococci colonizing the tongue and cheek possess different ribosomally synthesized and posttranslationally modified peptide BGCs. Finally, we highlight bacterial genera with BGCs but are underexplored for specialized metabolism and demonstrate the bioactivity of Actinomyces against other bacteria, including human pathogens. Together, our results demonstrate that specialized metabolism in the ADT is extensive and that by exploring these microbiomes further, we will better understand the ecology and biogeography of this system and identify new bioactive natural products. IMPORTANCE Bacteria produce specialized metabolites to compete with other microbes. Though the biological activities of many specialized metabolites have been determined, our understanding of their ecology is limited, particularly within the human microbiome. As the aerodigestive tract (ADT) faces the external environment, bacteria colonizing this tract must compete both among themselves and with invading microbes, including human pathogens. We analyzed the genomes of ADT bacteria to identify biosynthetic gene clusters (BGCs) for specialized metabolites. We found that the majority of ADT BGCs are uncharacterized and the metabolites they encode are unknown. We mapped the distribution of BGCs across the ADT and determined that each site is associated with its own distinct bacterial community and BGCs. By further characterizing these BGCs, we will inform our understanding of ecology and biogeography across the ADT, and we may uncover new specialized metabolites, including antibiotics.
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Oftedal TF, Ovchinnikov KV, Hestad KA, Goldbeck O, Porcellato D, Narvhus J, Riedel CU, Kjos M, Diep DB. Ubericin K, a New Pore-Forming Bacteriocin Targeting mannose-PTS. Microbiol Spectr 2021; 9:e0029921. [PMID: 34643411 PMCID: PMC8515946 DOI: 10.1128/spectrum.00299-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/10/2021] [Indexed: 11/20/2022] Open
Abstract
Bovine mastitis infection in dairy cattle is a significant economic burden for the dairy industry globally. To reduce the use of antibiotics in treatment of clinical mastitis, new alternative treatment options are needed. Antimicrobial peptides from bacteria, also known as bacteriocins, are potential alternatives for combating mastitis pathogens. In search of novel bacteriocins against mastitis pathogens, we screened samples of Norwegian bovine raw milk and found a Streptococcus uberis strain with potent antimicrobial activity toward Enterococcus, Streptococcus, Listeria, and Lactococcus. Whole-genome sequencing of the strain revealed a multibacteriocin gene cluster encoding one class IIb bacteriocin, two class IId bacteriocins, in addition to a three-component regulatory system and a dedicated ABC transporter. Isolation and purification of the antimicrobial activity from culture supernatants resulted in the detection of a 6.3-kDa mass peak by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry, a mass corresponding to the predicted size of one of the class IId bacteriocins. The identification of this bacteriocin, called ubericin K, was further confirmed by in vitro protein synthesis, which showed the same inhibitory spectrum as the purified antimicrobial compound. Ubericin K shows highest sequence similarity to the class IId bacteriocins bovicin 255, lactococcin A, and garvieacin Q. We found that ubericin K uses the sugar transporter mannose phosphotransferase (PTS) as a target receptor. Further, by using the pHlourin sensor system to detect intracellular pH changes due to leakage across the membrane, ubericin K was shown to be a pore former, killing target cells by membrane disruption. IMPORTANCE Bacterial infections in dairy cows are a major burden to farmers worldwide because infected cows require expensive treatments and produce less milk. Today, infected cows are treated with antibiotics, a practice that is becoming less effective due to antibiotic resistance. Compounds other than antibiotics also exist that kill bacteria causing infections in cows; these compounds, known as bacteriocins, are natural products produced by other bacteria in the environment. In this work, we discover a new bacteriocin that we call ubericin K, which kills several species of bacteria known to cause infections in dairy cows. We also use in vitro synthesis as a novel method for rapidly characterizing bacteriocins directly from genomic data, which could be useful for other researchers. We believe that ubericin K and the methods described in this work will aid in the transition away from antibiotics in the dairy industry.
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Affiliation(s)
- Thomas F. Oftedal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Kirill V. Ovchinnikov
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Kai A. Hestad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Oliver Goldbeck
- Institute of Microbiology and Biotechnology, Ulm University, Ulm, Germany
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Judith Narvhus
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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10
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Twomey E, Hill C, Field D, Begley M. Recipe for Success: Suggestions and Recommendations for the Isolation and Characterisation of Bacteriocins. Int J Microbiol 2021; 2021:9990635. [PMID: 34257667 PMCID: PMC8249226 DOI: 10.1155/2021/9990635] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/17/2021] [Accepted: 06/09/2021] [Indexed: 12/29/2022] Open
Abstract
Bacteriocins are bacterially produced antimicrobial peptides. Although only two peptides have been approved for use as natural preservatives foods, current research is focusing on expanding their application as potential therapeutics against clinical pathogens. Our laboratory group has been working on bacteriocins for over 25 years, and during that time, we have isolated bacteriocin-producing microorganisms from a variety of sources including human skin, human faeces, and various foods. These bacteriocins were purified and characterised, and their potential applications were examined. We have also identified bioengineered derivatives of the prototype lantibiotic nisin which possess more desirable properties than the wild-type, such as enhanced antimicrobial activity. In the current communication, we discuss the main methods that were employed to identify such peptides. Furthermore, we provide a step-by-step guide to carrying out these methods that include accompanying diagrams. We hope that our recommendations and advice will be of use to others in their search for, and subsequent analysis of, novel bacteriocins, and derivatives thereof.
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Affiliation(s)
- Ellen Twomey
- Department of Biological Sciences, Munster Technological University, Cork T12 P928, Ireland
| | - Colin Hill
- School of Microbiology, University College Cork, Cork T12YT20, Ireland
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland
| | - Des Field
- School of Microbiology, University College Cork, Cork T12YT20, Ireland
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland
| | - Máire Begley
- Department of Biological Sciences, Munster Technological University, Cork T12 P928, Ireland
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11
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Lee K, Kaspar JR, Rojas-Carreño G, Walker AR, Burne RA. A single system detects and protects the beneficial oral bacterium Streptococcus sp. A12 from a spectrum of antimicrobial peptides. Mol Microbiol 2021; 116:211-230. [PMID: 33590560 DOI: 10.1111/mmi.14703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/11/2021] [Accepted: 02/11/2021] [Indexed: 10/22/2022]
Abstract
The commensal bacterium Streptococcus sp. A12 has multiple properties that may promote the stability of health-associated oral biofilms, including overt antagonism of the dental caries pathogen Streptococcus mutans. A LanFEG-type ABC transporter, PcfFEG, confers tolerance to the lantibiotic nisin and enhances the ability of A12 to compete against S. mutans. Here, we investigated the regulation of pcfFEG and adjacent genes for a two-component system, pcfRK, to better understand antimicrobial peptide resistance by A12. Induction of pcfFEG-pcfRK was the primary mechanism to respond rapidly to nisin. In addition to nisin, PcfFEG conferred tolerance by A12 to a spectrum of lantibiotic and non-lantibiotic antimicrobial peptides produced by a diverse collection of S. mutans isolates. Loss of PcfFEG resulted in the altered spatio-temporal arrangement of A12 and S. mutans in a dual-species biofilm model. Deletion of PcfFEG or PcfK resulted in constitutive activation of pcfFEG and expression of pcfFEG was inhibited by small peptides in the pcfK mutant. Transcriptional profiling of pcfR or pcfK mutants combined with functional genomics revealed peculiarities in PcfK function and a novel panel of genes responsive to nisin. Collectively, the results provide fundamental insights that strengthen the foundation for the design of microbial-based therapeutics to control oral infectious diseases.
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Affiliation(s)
- Kyulim Lee
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Justin R Kaspar
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA.,Division of Biosciences, College of Dentistry, Ohio State University, Columbus, OH, USA
| | - Gisela Rojas-Carreño
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Alejandro R Walker
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Robert A Burne
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
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12
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Torres MDT, Cao J, Franco OL, Lu TK, de la Fuente-Nunez C. Synthetic Biology and Computer-Based Frameworks for Antimicrobial Peptide Discovery. ACS NANO 2021; 15:2143-2164. [PMID: 33538585 PMCID: PMC8734659 DOI: 10.1021/acsnano.0c09509] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Antibiotic resistance is one of the greatest challenges of our time. This global health problem originated from a paucity of truly effective antibiotic classes and an increased incidence of multi-drug-resistant bacterial isolates in hospitals worldwide. Indeed, it has been recently estimated that 10 million people will die annually from drug-resistant infections by the year 2050. Therefore, the need to develop out-of-the-box strategies to combat antibiotic resistance is urgent. The biological world has provided natural templates, called antimicrobial peptides (AMPs), which exhibit multiple intrinsic medical properties including the targeting of bacteria. AMPs can be used as scaffolds and, via engineering, can be reconfigured for optimized potency and targetability toward drug-resistant pathogens. Here, we review the recent development of tools for the discovery, design, and production of AMPs and propose that the future of peptide drug discovery will involve the convergence of computational and synthetic biology principles.
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Affiliation(s)
- Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jicong Cao
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Octavio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, DF 70790160, Brazil
- S-inova Biotech, Universidade Católica Dom Bosco, Campo Grande, MS 79117010, Brazil
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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13
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Abstract
Gram-positive bacteria employ an array of secreted peptides to control population-level behaviors in response to environmental cues. We review mechanistic and functional features of secreted peptides produced by the human pathogen Streptococcus pneumoniae. We discuss sequence features, mechanisms of transport, and receptors for 3 major categories of small peptides: the double-glycine peptides, the Rap, Rgg, NprR, PlcR, and PrgX (RRNPP)-binding peptides, and the lanthionine-containing peptides. We highlight the impact of factors that contribute to carriage and pathogenesis, specifically genetic diversity, microbial competition, biofilm development, and environmental adaptation. A recent expansion in pneumococcal peptide studies reveals a complex network of interacting signaling systems where multiple peptides are integrated into the same signaling pathway, allowing multiple points of entry into the pathway and extending information content in new directions. In addition, since peptides are present in the extracellular milieu, there are opportunities for crosstalk, quorum sensing (QS), as well as intra- and interstrain and species interactions. Knowledge on the manner that population-level behaviors contribute to disease provides an avenue for the design and development of anti-infective strategies.
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14
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Novel Probiotic Mechanisms of the Oral Bacterium Streptococcus sp. A12 as Explored with Functional Genomics. Appl Environ Microbiol 2019; 85:AEM.01335-19. [PMID: 31420345 DOI: 10.1128/aem.01335-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/14/2019] [Indexed: 12/11/2022] Open
Abstract
Health-associated biofilms in the oral cavity are composed of a diverse group of microbial species that can foster an environment that is less favorable for the outgrowth of dental caries pathogens, like Streptococcus mutans A novel oral bacterium, designated Streptococcus A12, was previously isolated from supragingival dental plaque of a caries-free individual and was shown to interfere potently with the growth and virulence properties of S. mutans In this study, we applied functional genomics to begin to identify molecular mechanisms used by A12 to antagonize, and to resist the antagonistic factors of, S. mutans Using bioinformatics, genes that could encode factors that enhance the ability of A12 to compete with S. mutans were identified. Selected genes, designated potential competitive factors (pcf), were deleted. Certain mutant derivatives showed a reduced capacity to compete with S. mutans compared to that of the parental strain. The A12 pcfO mutant lost the ability to inhibit comX -inducing peptide (XIP) signaling by S. mutans, while mutants with changes in the pcfFEG locus were impaired in sensing of, and were more sensitive to, the lantibiotic nisin. Loss of PcfV, annotated as a colicin V biosynthetic protein, resulted in diminished antagonism of S. mutans Collectively, the data provide new insights into the complexities and variety of factors that affect biofilm ecology and virulence. Continued exploration of the genomic and physiological factors that distinguish commensals from truly beneficial members of the oral microbiota will lead to a better understanding of the microbiome and new approaches to promote oral health.IMPORTANCE Advances in defining the composition of health-associated biofilms have highlighted the important role of beneficial species in maintaining health. Comparatively little, however, has been done to address the genomic and physiological bases underlying the probiotic mechanisms of beneficial commensals. In this study, we explored the ability of a novel oral bacterial isolate, Streptococcus A12, to compete with the dental pathogen Streptococcus mutans using various gene products with diverse functions. A12 displayed enhanced competitiveness by (i) disrupting intercellular communication pathways of S. mutans, (ii) sensing and resisting antimicrobial peptides, and (iii) producing factors involved in the production of a putative antimicrobial compound. Research on the probiotic mechanisms employed by Streptococcus A12 is providing essential insights into how beneficial bacteria may help maintain oral health, which will aid in the development of biomarkers and therapeutics that can improve the practice of clinical dentistry.
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15
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Motib AS, Al-Bayati FAY, Manzoor I, Shafeeq S, Kadam A, Kuipers OP, Hiller NL, Andrew PW, Yesilkaya H. TprA/PhrA Quorum Sensing System Has a Major Effect on Pneumococcal Survival in Respiratory Tract and Blood, and Its Activity Is Controlled by CcpA and GlnR. Front Cell Infect Microbiol 2019; 9:326. [PMID: 31572692 PMCID: PMC6753895 DOI: 10.3389/fcimb.2019.00326] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/29/2019] [Indexed: 12/25/2022] Open
Abstract
Streptococcus pneumoniae is able to cause deadly diseases by infecting different tissues, each with distinct environmental and nutritional compositions. We hypothesize that the adaptive capabilities of the microbe is an important facet of pneumococcal survival in fluctuating host environments. Quorum-sensing (QS) mechanisms are pivotal for microbial host adaptation. We previously demonstrated that the TprA/PhrA QS system is required for pneumococcal utilization of galactose and mannose, neuraminidase activity, and virulence. We also showed that the system can be modulated by using linear molecularly imprinted polymers. Due to being a drugable target, we further studied the operation of this QS system in S. pneumoniae. We found that TprA controls the expression of nine different operons on galactose and mannose. Our data revealed that TprA expression is modulated by a complex regulatory network, where the master regulators CcpA and GlnR are involved in a sugar dependent manner. Mutants in the TprA/PhrA system are highly attenuated in their survival in nasopharynx and lungs after intranasal infection, and growth in blood after intravenous infection.
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Affiliation(s)
- Anfal Shakir Motib
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, United Kingdom.,Department of Microbiology, College of Medicine, University of Diyala, Baqubah, Iraq
| | - Firas A Y Al-Bayati
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, United Kingdom.,College of Pharmacy, University of Kirkuk, Kirkuk, Iraq
| | - Irfan Manzoor
- Molecular Genetics, University of Groningen, Groningen, Netherlands
| | - Sulman Shafeeq
- Molecular Genetics, University of Groningen, Groningen, Netherlands
| | - Anagha Kadam
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Oscar P Kuipers
- Molecular Genetics, University of Groningen, Groningen, Netherlands
| | - N Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Peter W Andrew
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, United Kingdom
| | - Hasan Yesilkaya
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, United Kingdom
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16
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Shen P, Lees JA, Bee GCW, Brown SP, Weiser JN. Pneumococcal quorum sensing drives an asymmetric owner-intruder competitive strategy during carriage via the competence regulon. Nat Microbiol 2018; 4:198-208. [PMID: 30546100 DOI: 10.1038/s41564-018-0314-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/30/2018] [Indexed: 11/09/2022]
Abstract
Competition among microorganisms is a key determinant of successful host colonization and persistence. For Streptococcus pneumoniae, lower than predicted rates of co-colonizing strains suggest a competitive advantage for resident bacteria over newcomers. In light of evolutionary theory, we hypothesized that S. pneumoniae use owner-intruder asymmetries to settle contests, leading to the disproportionate success of the initial resident 'owner', regardless of the genetic identity of the 'intruder'. We investigated the determinants of within-host competitive success utilizing S. pneumoniae colonization of the upper respiratory tract of infant mice. Within 6 h, colonization by the resident inhibited colonization by an isogenic challenger. The competitive advantage of the resident was dependent on quorum sensing via the competence (Com) regulon and downstream choline binding protein D (CbpD) and on the competence-induced bacteriocins A and B (CibAB) implicated in fratricide. CbpD and CibAB are highly conserved across pneumococcal lineages, indicating evolutionary advantages for asymmetric competitive strategies within the species. Mathematical modelling supported a significant role for quorum sensing via the Com regulon in competition, even for strains with different competitive advantages. Our study suggests that asymmetric owner-intruder competitive strategies do not require complex cognition and are used by a major human pathogen to determine 'ownership' of human hosts.
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Affiliation(s)
- Pamela Shen
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - John A Lees
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Gavyn Chern Wei Bee
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Sam P Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jeffrey N Weiser
- Department of Microbiology, New York University School of Medicine, New York, NY, USA.
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17
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Wibowo D, Zhao CX. Recent achievements and perspectives for large-scale recombinant production of antimicrobial peptides. Appl Microbiol Biotechnol 2018; 103:659-671. [DOI: 10.1007/s00253-018-9524-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/10/2018] [Accepted: 11/14/2018] [Indexed: 02/07/2023]
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