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Naknaen A, Surachat K, Manit J, Jetwanna KWN, Thawonsuwan J, Pomwised R. Virulent properties and genomic diversity of Vibrio vulnificus isolated from environment, human, diseased fish. Microbiol Spectr 2024; 12:e0007924. [PMID: 38860819 PMCID: PMC11218479 DOI: 10.1128/spectrum.00079-24] [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: 01/18/2024] [Accepted: 05/02/2024] [Indexed: 06/12/2024] Open
Abstract
The incidence of Vibrio vulnificus infections, with high mortality rates in humans and aquatic animals, has escalated, highlighting a significant public health challenge. Currently, reliable markers to identify strains with high virulence potential are lacking, and the understanding of evolutionary drivers behind the emergence of pathogenic strains is limited. In this study, we analyzed the distribution of virulent genotypes and phenotypes to discern the infectious potential of V. vulnificus strains isolated from three distinct sources. Most isolates, traditionally classified as biotype 1, possessed the virulence-correlated gene-C type. Environmental isolates predominantly exhibited YJ-like alleles, while clinical and diseased fish isolates were significantly associated with the nanA gene and pathogenicity region XII. Hemolytic activity was primarily observed in the culture supernatants of clinical and diseased fish isolates. Genetic relationships, as determined by multiple-locus variable-number tandem repeat analysis, suggested that strains originating from the same source tended to cluster together. However, multilocus sequence typing revealed considerable genetic diversity across clusters and sources. A phylogenetic analysis using single nucleotide polymorphisms of diseased fish strains alongside publicly available genomes demonstrated a high degree of evolutionary relatedness within and across different isolation sources. Notably, our findings reveal no direct correlation between phylogenetic patterns, isolation sources, and virulence capabilities. This underscores the necessity for proactive risk management strategies to address pathogenic V. vulnificus strains emerging from environmental reservoirs.IMPORTANCEAs the global incidence of Vibrio vulnificus infections rises, impacting human health and marine aquacultures, understanding the pathogenicity of environmental strains remains critical yet underexplored. This study addresses this gap by evaluating the virulence potential and genetic relatedness of V. vulnificus strains, focusing on environmental origins. We conduct an extensive genotypic analysis and phenotypic assessment, including virulence testing in a wax moth model. Our findings aim to uncover genetic and evolutionary factors that drive pathogenic strain emergence in the environment. This research advances our ability to identify reliable virulence markers and understand the distribution of pathogenic strains, offering significant insights for public health and environmental risk management.
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Affiliation(s)
- Ampapan Naknaen
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Jutamas Manit
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | | | - Jumroensri Thawonsuwan
- Department of Fisheries, Aquatic Animal Health Research and Development Division, Songkhla Aquatic Animal Health Research Center, Songkhla, Thailand
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
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Arce M, Venegas G, Paez K, Latz S, Navarrete P, Caruffo M, Feijoo C, García K, Bastías R. Valp1, a Newly Identified Temperate Phage Facilitating Coexistence of Lysogenic and Non-Lysogenic Populations of Vibrio anguillarum. Pathogens 2024; 13:285. [PMID: 38668240 PMCID: PMC11054321 DOI: 10.3390/pathogens13040285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/23/2024] [Accepted: 03/24/2024] [Indexed: 04/29/2024] Open
Abstract
Vibrio anguillarum is a pathogen for several fish and shellfish species. Its ecology is influenced by diverse factors, including bacteriophages. Here, we identify and characterize a new temperate bacteriophage (Valp1) of V. anguillarum. Valp1 is a myovirus with a 60 nm head and a 90 nm contractile tail. Its double-stranded DNA genome of 42,988 bp contains 68 genes, including a protelomerase gene, typical of telomeric phages. Valp1 inhibits the growth of the virulent strain of V. anguillarum PF4, while the derived lysogenic strain P1.1 presents a slight reduction in its growth but is not affected by the presence of Valp1. Both strains present similar virulence in a larval zebrafish (Danio rerio) model, and only slight differences have been observed in their biochemical profile. Co-culture assays reveal that PF4 and P1.1 can coexist for 10 h in the presence of naturally induced Valp1, with the proportion of PF4 ranging between 28% and 1.6%. By the end of the assay, the phage reached a concentration of ~108 PFU/mL, and all the non-lysogenic PF4 strains were resistant to Valp1. This equilibrium was maintained even after five successive subcultures, suggesting the existence of a coexistence mechanism between the lysogenic and non-lysogenic populations of V. anguillarum in conjunction with the phage Valp1.
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Affiliation(s)
- Manuel Arce
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile; (M.A.)
| | - Guillermo Venegas
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile; (M.A.)
| | - Karla Paez
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile; (M.A.)
| | - Simone Latz
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile; (M.A.)
| | - Paola Navarrete
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago 7830490, Chile
| | - Mario Caruffo
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago 7830490, Chile
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820000, Chile
| | - Carmen Feijoo
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370146, Chile
| | - Katherine García
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8910060, Chile
| | - Roberto Bastías
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile; (M.A.)
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Pandey R, Sharma S, Sinha KK. Evidence of Antibiotic Resistance and Virulence Factors in Environmental Isolates of Vibrio Species. Antibiotics (Basel) 2023; 12:1062. [PMID: 37370381 DOI: 10.3390/antibiotics12061062] [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: 05/01/2023] [Revised: 06/03/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
The outbreak of waterborne diseases such as cholera and non-cholera (vibriosis) is continuously increasing in the environment due to fecal and sewage discharge in water sources. Cholera and vibriosis are caused by different species of Vibrio genus which are responsible for acute diarrheal disease and soft tissue damage. Although incidences of cholera and vibriosis have been reported from the Vaishali district of Bihar, India, clinical or environmental strains have not been characterized in this region. Out of fifty environmental water samples, twelve different biochemical test results confirmed the presence of twenty Vibrio isolates. The isolates were found to belong to five different Vibrio species, namely V. proteolyticus, V. campbellii, V. nereis, V. cincinnatiensis, and V. harveyi. From the identified isolates, 65% and 45% isolates were found to be resistant to ampicillin and cephalexin, respectively. Additionally, two isolates were found to be resistant against six and four separately selected antibiotics. Furthermore, virulent hlyA and ompW genes were detected by PCR in two different isolates. Additionally, phage induction was also noticed in two different isolates which carry lysogenic phage in their genome. Overall, the results reported the identification of five different Vibrio species in environmental water samples. The isolates showed multiple antibacterial resistance, phage induction, and virulence gene profile in their genome.
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Affiliation(s)
- Rajkishor Pandey
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur 844102, Bihar, India
- School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Simran Sharma
- Department of Basic and Applied Sciences, National Institute of Food Technology Entrepreneurship & Management (NIFTEM), Kundli, Sonipat 131028, Haryana, India
| | - Kislay Kumar Sinha
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur 844102, Bihar, India
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Li Z, Bao X, Liu X, Wang W, Yang J. Gene network analyses of larvae under different egg-protecting behaviors provide novel insights into immune response mechanisms of Amphioctopus fangsiao. FISH & SHELLFISH IMMUNOLOGY 2023; 136:108733. [PMID: 37028690 DOI: 10.1016/j.fsi.2023.108733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/28/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
Amphioctopus fangsiao was a representative economic species in cephalopods, which was vulnerable to marine bacteria. Vibrio anguillarum was a highly infectious pathogen that have recently been found to infect A. fangsiao and inhibit its growth and development. There were significant differences in the immune response mechanisms between egg-protected and egg-unprotected larvae. To explore larval immunity under different egg-protecting behaviors, we infected A. fangsiao larvae with V. anguillarum for 24 h and analyzed the transcriptome data about egg-protected and egg-unprotected larvae infected with 0, 4, 12, and 24 h using weighted gene co-expression networks (WGCNA) and protein-protein interaction (PPI) networks. Network analyses revealed a series of immune response processes after infection, and identified six key modules and multiple immune-related hub genes. Meanwhile, we found that ZNF family, such as ZNF32, ZNF160, ZNF271, ZNF479, and ZNF493 might play significant roles in A. fangsiao immune response processes. We first creatively combined WGCNA and PPI network analysis to deeply explore the immune response mechanisms of A. fangsiao larvae with different egg-protecting behaviors. Our results provided further insights into the immunity of V. anguillarum infected invertebrates, and laid the foundation for exploring the immune differences among cephalopods with different egg protecting behaviors.
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Affiliation(s)
- Zan Li
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiaokai Bao
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Weijun Wang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai, 264025, China.
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5
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Molina-Quiroz RC, Silva-Valenzuela CA. Interactions of Vibrio phages and their hosts in aquatic environments. Curr Opin Microbiol 2023; 74:102308. [PMID: 37062175 DOI: 10.1016/j.mib.2023.102308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 04/18/2023]
Abstract
Bacteriophages (phages) are viruses that specifically infect bacteria. These viruses were discovered a century ago and have been used as a model system in microbial genetics and molecular biology. In order to survive, bacteria have to quickly adapt to phage challenges in their natural settings. In turn, phages continuously develop/evolve mechanisms for battling host defenses. A deeper understanding of the arms race between bacteria and phages is essential for the rational design of phage-based prophylaxis and therapies to prevent and treat bacterial infections. Vibrio species and their phages (vibriophages) are a suitable model to study these interactions. Phages are highly ubiquitous in aquatic environments and Vibrio are waterborne bacteria that must survive the constant attack by phages for successful transmission to their hosts. Here, we review relevant literature from the past two years to delve into the molecular interactions of Vibrio species and their phages in aquatic niches.
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Affiliation(s)
- Roberto C Molina-Quiroz
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts Medical Center and Tufts University, Boston, MA, USA
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6
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Staying below the Radar: Unraveling a New Family of Ubiquitous "Cryptic" Non-Tailed Temperate Vibriophages and Implications for Their Bacterial Hosts. Int J Mol Sci 2023; 24:ijms24043937. [PMID: 36835353 PMCID: PMC9966536 DOI: 10.3390/ijms24043937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/18/2023] Open
Abstract
Bacteriophages are the most abundant biological entities in the oceans and play key roles in bacterial activity, diversity and evolution. While extensive research has been conducted on the role of tailed viruses (Class: Caudoviricetes), very little is known about the distribution and functions of the non-tailed viruses (Class: Tectiliviricetes). The recent discovery of the lytic Autolykiviridae family demonstrated the potential importance of this structural lineage, emphasizing the need for further exploration of the role of this group of marine viruses. Here, we report the novel family of temperate phages under the class of Tectiliviricetes, which we propose to name "Asemoviridae" with phage NO16 as a main representative. These phages are widely distributed across geographical regions and isolation sources and found inside the genomes of at least 30 species of Vibrio, in addition to the original V. anguillarum isolation host. Genomic analysis identified dif-like sites, suggesting that NO16 prophages recombine with the bacterial genome based on the XerCD site-specific recombination mechanism. The interactions between the NO16 phage and its V. anguillarum host were linked to cell density and phage-host ratio. High cell density and low phage predation levels were shown to favor the temperate over the lytic lifestyle for NO16 viruses, and their spontaneous induction rate was highly variable between different V. anguillarum lysogenic strains. NO16 prophages coexist with the V. anguillarum host in a mutualistic interaction by rendering fitness properties to the host, such as increased virulence and biofilm formation through lysogenic conversion, likely contributing to their global distribution.
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Qi Q, Rajabal V, Ghaly TM, Tetu SG, Gillings MR. Identification of integrons and gene cassette-associated recombination sites in bacteriophage genomes. Front Microbiol 2023; 14:1091391. [PMID: 36744093 PMCID: PMC9892861 DOI: 10.3389/fmicb.2023.1091391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
Bacteriophages are versatile mobile genetic elements that play key roles in driving the evolution of their bacterial hosts through horizontal gene transfer. Phages co-evolve with their bacterial hosts and have plastic genomes with extensive mosaicism. In this study, we present bioinformatic and experimental evidence that temperate and virulent (lytic) phages carry integrons, including integron-integrase genes, attC/attI recombination sites and gene cassettes. Integrons are normally found in Bacteria, where they capture, express and re-arrange mobile gene cassettes via integron-integrase activity. We demonstrate experimentally that a panel of attC sites carried in virulent phage can be recognized by the bacterial class 1 integron-integrase (IntI1) and then integrated into the paradigmatic attI1 recombination site using an attC x attI recombination assay. With an increasing number of phage genomes projected to become available, more phage-associated integrons and their components will likely be identified in the future. The discovery of integron components in bacteriophages establishes a new route for lateral transfer of these elements and their cargo genes between bacterial host cells.
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Affiliation(s)
- Qin Qi
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia,*Correspondence: Qin Qi, ✉
| | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Timothy M. Ghaly
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sasha G. Tetu
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Michael R. Gillings
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
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Molina-Quiroz RC, Camilli A, Silva-Valenzuela CA. Role of Bacteriophages in the Evolution of Pathogenic Vibrios and Lessons for Phage Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:149-173. [PMID: 36792875 PMCID: PMC10587905 DOI: 10.1007/978-3-031-22997-8_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Viruses of bacteria, i.e., bacteriophages (or phages for short), were discovered over a century ago and have played a major role as a model system for the establishment of the fields of microbial genetics and molecular biology. Despite the relative simplicity of phages, microbiologists are continually discovering new aspects of their biology including mechanisms for battling host defenses. In turn, novel mechanisms of host defense against phages are being discovered at a rapid clip. A deeper understanding of the arms race between bacteria and phages will continue to reveal novel molecular mechanisms and will be important for the rational design of phage-based prophylaxis and therapies to prevent and treat bacterial infections, respectively. Here we delve into the molecular interactions of Vibrio species and phages.
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Affiliation(s)
- Roberto C Molina-Quiroz
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts Medical Center and Tufts University, Boston, MA, USA
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University, School of Medicine, Boston, MA, USA
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Donati VL, Madsen L, Middelboe M, Strube ML, Dalsgaard I. The Gut Microbiota of Healthy and Flavobacterium psychrophilum-Infected Rainbow Trout Fry Is Shaped by Antibiotics and Phage Therapies. Front Microbiol 2022; 13:771296. [PMID: 35620089 PMCID: PMC9128845 DOI: 10.3389/fmicb.2022.771296] [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: 09/06/2021] [Accepted: 03/07/2022] [Indexed: 01/15/2023] Open
Abstract
In the aquaculture sector, there is an increased interest in developing environmentally friendly alternatives to antibiotics in the treatment and prevention of bacterial infections. This requires an understanding of the effects of different treatments on the fish microbiota as a measure for improving the fish health status. In this study, we focused on the freshwater pathogen Flavobacterium psychrophilum and investigated the effects of antibiotics (florfenicol) and phage therapies on the gut microbiota of healthy and infected rainbow trout fry (1–2 g). Florfenicol-coated feed was administered for 10 days, starting two days after the infection procedure. A two-component mix of phage targeting F. psychrophilum (FpV4 and FPSV-D22) was continuously delivered by feed with a prophylactic period of 12 days. Samples of the distal intestine were collected over time (day -1 and 1, 8, and 33 days post-infection) and analyzed by community analysis targeting the 16S rRNA gene (V3–V4 region). Results showed the dysbiosis effect caused both by the infection and by florfenicol administration. Shifts in the overall composition were detected by β-diversity analysis, and changes in specific populations were observed during taxonomic mapping. Measures of α-diversity were only affected in infected fish (large variation observed 1 and 8 dpi). These community alterations disappeared again when fish recovered from the infection and the antibiotic treatment was terminated (33 dpi). Interestingly, phage addition altered the microbiota of the fish independently of the presence of their target bacterium. The overall gut bacterial community in fish fed phage-treated feed was different from the controls at each time point as revealed by β-diversity analysis. However, it was not possible to identify specific bacterial populations responsible for these changes except for an increase of lactic acid bacteria 33 dpi. Overall, the results indicate that the administered phages might affect the complex network of phage-bacteria interactions in the fish gut. Nevertheless, we did not observe negative effects on fish health or growth, and further studies should be directed in understanding if these changes are beneficial or not for the fish health with an additional focus on the host immune response.
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Affiliation(s)
- Valentina Laura Donati
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lone Madsen
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Inger Dalsgaard
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
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Nawel Z, Rima O, Amira B. An overview on Vibrio temperate phages: Integration mechanisms, pathogenicity, and lysogeny regulation. Microb Pathog 2022; 165:105490. [DOI: 10.1016/j.micpath.2022.105490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/21/2022]
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Castillo D, Højsting AR, Roosvall A, Smyrlis G, Jørgensen J, Middelboe M. In Vitro Evolution of Specific Phages Infecting the Fish Pathogen Flavobacterium psychrophilum. PHAGE 2022; 3:28-37. [PMID: 37025924 PMCID: PMC10071593 DOI: 10.1089/phage.2022.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Background Flavobacterium psychrophilum is the causative agent of the bacterial cold-water disease and rainbow trout fry syndrome. Owing to the issues associated with increasing use of antibiotics to control the diseases, phage therapy has been proposed as an alternative method to control Flavobacterium infection within the industry. Materials and Methods We explored two simple and fast in vitro strategies for the isolation of evolved F. psychrophilum phages, using three well-characterized phages FpV4, FpV9, and FPSV-S20. Results During in vitro serial transfer experiments, 12 evolved phages were selected 72-96 h after phage exposure in the first or second week. Phenotype analysis showed improvement of host range and efficiency of plating and adsorption constants. Comparative genomic analysis of the evolved phages identified 13 independent point mutations causing amino acid changes mostly in hypothetical proteins. Conclusions These results confirmed the reliability and effectivity of two strategies to isolate evolved F. psychrophilum phages, which may be used to expand phage-host range and target phage-resistant pathogens in phage therapy applications against Flavobacterium infections.
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Affiliation(s)
- Daniel Castillo
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
- Instituto de Investigación Interdisciplinar en Ciencias Biomédicas SEK (I3CBSEK), Universidad SEK, Santiago, Chile
| | | | - Andrea Roosvall
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Giorgos Smyrlis
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Johanna Jørgensen
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Mathias Middelboe
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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12
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Hosseini N, Paquet VE, Chehreghani M, Moineau S, Charette SJ. Phage Cocktail Development against Aeromonas salmonicida subsp. salmonicida Strains Is Compromised by a Prophage. Viruses 2021; 13:2241. [PMID: 34835047 PMCID: PMC8621227 DOI: 10.3390/v13112241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/22/2021] [Accepted: 11/04/2021] [Indexed: 11/17/2022] Open
Abstract
Aquaculture is a rapidly growing food production sector. Fish farmers are experiencing increasing problems with antibiotic resistance when fighting against pathogenic bacteria such as Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis. Phage therapy may provide an alternative, but effective use must be determined. Here, we studied the inhibition of A. salmonicida subsp. salmonicida strains by five phages (HER98 [44RR2.8t.2], HER110 [65.2], SW69-9, L9-6 and Riv-10) used individually or as combinations of two to five phages. A particular combination of four phages (HER98 [44RR2.8t.2], SW69-9, Riv-10, and HER110 [65.2]) was found to be the most effective when used at an initial multiplicity of infection (MOI) of 1 against the A. salmonicida subsp. salmonicida strain 01-B526. The same phage cocktail is effective against other strains except those bearing a prophage (named Prophage 3), which is present in 2/3 of the strains from the province of Quebec. To confirm the impact of this prophage, we tested the effectiveness of the same cocktail on strains that were either cured or lysogenized with Prophage 3. While the parental strains were sensitive to the phage cocktail, the lysogenized ones were much less sensitive. These data indicate that the prophage content of A. salmonicida subsp. salmonicida can affect the efficacy of a cocktail of virulent phages for phage therapy purposes.
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Affiliation(s)
- Nava Hosseini
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada; (N.H.); (V.E.P.); (S.M.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC G1V 4G5, Canada
| | - Valérie E. Paquet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada; (N.H.); (V.E.P.); (S.M.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC G1V 4G5, Canada
| | - Mahdi Chehreghani
- Department of Mechanical Engineering, McGill University, Montreal, QC H3A 0C3, Canada;
| | - Sylvain Moineau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada; (N.H.); (V.E.P.); (S.M.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de Médecine Dentaire, Université Laval, Quebec City, QC G1V 0A6, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Steve J. Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada; (N.H.); (V.E.P.); (S.M.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC G1V 4G5, Canada
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13
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Daniel C, Johanna J, Krister S, Lone M, Inger D, Tom W, Mathias M. Genome-informed approach to identify genetic determinants of Flavobacterium psychrophilum phage susceptibility. Environ Microbiol 2021; 23:4185-4199. [PMID: 33989443 DOI: 10.1111/1462-2920.15593] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/08/2021] [Accepted: 05/11/2021] [Indexed: 12/17/2022]
Abstract
The fish pathogen Flavobacterium psychrophilum infects farmed salmonids worldwide, and application of bacteriophages has been suggested for controlling disease outbreaks in aquaculture. Successful application of phages requires detailed knowledge about the variability in phage susceptibility of the host communities. In this study, we analysed the genetic diversity of F. psychrophilum hosts and phages from the Baltic Sea area to identify genetic determinants of phage-host interaction patterns. A host range analysis of 103 phages tested against 177 F. psychrophilum strains (18 231 phage-host interactions) identified nine phage clusters, infecting from 10% to 91% of the strain collection. The core genome-based comparison of 35 F. psychrophilum isolates revealed an extremely low overall genomic diversity (>99.5% similarity). However, a small subset of 16 ORFs, including genes involved in the type IX secretion system (T9SS), gliding motility and hypothetical cell-surface related proteins, exhibited a highly elevated genetic diversity. These specific genetic variations were linked to variability in phage infection patterns obtained from experimental studies, indicating that these genes are key determinants of phage susceptibility. These findings provide novel insights on the molecular mechanisms determining phage susceptibility in F. psychrophilum and emphasizes the importance of phages as drivers of core genomic diversity in this pathogen.
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Affiliation(s)
- Castillo Daniel
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.,Instituto de Investigación Interdisciplinar en Ciencias Biomédicas SEK (I3CBSEK), Universidad SEK, Santiago, Chile
| | - Jørgensen Johanna
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Sundell Krister
- Laboratory of Aquatic Pathobiology, Marine and Environmental Biology, Åbo Akademi University, Turku, Finland
| | - Madsen Lone
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dalsgaard Inger
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Wiklund Tom
- Laboratory of Aquatic Pathobiology, Marine and Environmental Biology, Åbo Akademi University, Turku, Finland
| | - Middelboe Mathias
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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14
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Donati VL, Dalsgaard I, Runtuvuori-Salmela A, Kunttu H, Jørgensen J, Castillo D, Sundberg LR, Middelboe M, Madsen L. Interactions between Rainbow Trout Eyed Eggs and Flavobacterium spp. Using a Bath Challenge Model: Preliminary Evaluation of Bacteriophages as Pathogen Control Agents. Microorganisms 2021; 9:971. [PMID: 33946270 PMCID: PMC8146780 DOI: 10.3390/microorganisms9050971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/10/2021] [Accepted: 04/14/2021] [Indexed: 11/17/2022] Open
Abstract
The microbial community surrounding fish eyed eggs can harbor pathogenic bacteria. In this study we focused on rainbow trout (Oncorhynchus mykiss) eyed eggs and the potential of bacteriophages against the pathogenic bacteria Flavobacterium psychrophilum and F. columnare. An infection bath method was first established, and the effects of singular phages on fish eggs was assessed (survival of eyed eggs, interaction of phages with eyed eggs). Subsequently, bacteria-challenged eyed eggs were exposed to phages to evaluate their effects in controlling the bacterial population. Culture-based methods were used to enumerate the number of bacteria and/or phages associated with eyed eggs and in the surrounding environment. The results of the study showed that, with our infection model, it was possible to re-isolate F. psychrophilum associated with eyed eggs after the infection procedure, without affecting the survival of the eggs in the short term. However, this was not possible for F. columnare, as this bacterium grows at higher temperatures than the ones recommended for incubation of rainbow trout eyed eggs. Bacteriophages do not appear to negatively affect the survival of rainbow trout eyed eggs and they do not seem to strongly adhere to the surface of eyed eggs either. Finally, the results demonstrated a strong potential for short term (24 h) phage control of F. psychrophilum. However, further studies are needed to explore if phage control can be maintained for a longer period and to further elucidate the mechanisms of interactions between Flavobacteria and their phages in association with fish eggs.
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Affiliation(s)
- Valentina L. Donati
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (I.D.); (L.M.)
| | - Inger Dalsgaard
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (I.D.); (L.M.)
| | - Anniina Runtuvuori-Salmela
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland; (A.R.-S.); (H.K.); (L.-R.S.)
| | - Heidi Kunttu
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland; (A.R.-S.); (H.K.); (L.-R.S.)
| | - Johanna Jørgensen
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark; (J.J.); (D.C.); (M.M.)
| | - Daniel Castillo
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark; (J.J.); (D.C.); (M.M.)
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland; (A.R.-S.); (H.K.); (L.-R.S.)
| | - Mathias Middelboe
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark; (J.J.); (D.C.); (M.M.)
| | - Lone Madsen
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (I.D.); (L.M.)
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15
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Donati VL, Dalsgaard I, Sundell K, Castillo D, Er-Rafik M, Clark J, Wiklund T, Middelboe M, Madsen L. Phage-Mediated Control of Flavobacterium psychrophilum in Aquaculture: In vivo Experiments to Compare Delivery Methods. Front Microbiol 2021; 12:628309. [PMID: 33763046 PMCID: PMC7983945 DOI: 10.3389/fmicb.2021.628309] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/15/2021] [Indexed: 12/31/2022] Open
Abstract
Phage-based approaches have gained increasing interest as sustainable alternative strategies to antibiotic treatment or as prophylactic measures against disease outbreaks in aquaculture. The potential of three methods (oral, bath, and injection) for delivering a two-component phage mixture to rainbow trout fry for controlling Flavobacterium psychrophilum infections and reduce fish mortality was investigated using bacteriophages FpV4 and FPSV-D22. For the oral administration experiment, bacteriophages were applied on feed pellets by spraying (1.6 × 108 PFU g-1) or by irreversible immobilization (8.3 × 107 PFU g-1), using the corona discharge technology (Fixed Phage Ltd.). The fish showed normal growth for every group and no mortality was observed prior to infection as well as in control groups during the infection. Constant detection of phages in the intestine (∼103 PFU mg-1) and more sporadic occurrence in kidney, spleen, and brain was observed. When fish were exposed to F. psychrophilum, no significant effect on fish survival, nor a direct impact on the number of phages in the sampled organs, were detected. Similarly, no significant increase in fish survival was detected when phages were delivered by bath (1st and 2nd bath: ∼106 PFU ml-1; 3rd bath: ∼105 PFU ml-1). However, when phages FpV4 and FPSV-D22 (1.7 × 108 PFU fish-1) were administered by intraperitoneal injection 3 days after the bacterial challenge, the final percent survival observed in the group injected with bacteriophages FpV4 and FPSV-D22 (80.0%) was significantly higher than in the control group (56.7%). The work demonstrates the delivery of phages to fish organs by oral administration, but also suggests that higher phage dosages than the tested ones may be needed on feed pellets to offer fish an adequate protection against F. psychrophilum infections.
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Affiliation(s)
- Valentina Laura Donati
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Inger Dalsgaard
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Krister Sundell
- Laboratory of Aquatic Pathobiology, Environmental and Marine Biology, Åbo Akademi University, Turku, Finland
| | - Daniel Castillo
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Mériem Er-Rafik
- National Centre for Nano Fabrication and Characterization, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Tom Wiklund
- Laboratory of Aquatic Pathobiology, Environmental and Marine Biology, Åbo Akademi University, Turku, Finland
| | - Mathias Middelboe
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lone Madsen
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
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16
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Kumar P, Sah AK, Tripathi G, Kashyap A, Tripathi A, Rao R, Mishra PC, Mallick K, Husain A, Kashyap MK. Role of ACE2 receptor and the landscape of treatment options from convalescent plasma therapy to the drug repurposing in COVID-19. Mol Cell Biochem 2021; 476:553-574. [PMID: 33029696 PMCID: PMC7539757 DOI: 10.1007/s11010-020-03924-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/19/2020] [Indexed: 02/06/2023]
Abstract
Since the first case reports in Wuhan, China, the SARS-CoV-2 has caused a pandemic and took lives of > 8,35,000 people globally. This single-stranded RNA virus uses Angiotensin-converting enzyme 2 (ACE2) as a receptor for entry into the host cell. Overexpression of ACE2 is mainly observed in hypertensive, diabetic and heart patients that make them prone to SARS-CoV-2 infection. Mitigations strategies were opted globally by the governments to minimize transmission of SARS-CoV-2 via the implementation of social distancing norms, wearing the facemasks, and spreading awareness using digital platforms. The lack of an approved drug treatment regimen, and non-availability of a vaccine, collectively posed a challenge for mankind to fight against the SARS-CoV-2 pandemic. In this scenario, repurposing of existing drugs and old treatment options like convalescent plasma therapy can be one of the potential alternatives to treat the disease. The drug repurposing provides a selection of drugs based on the scientific rationale and with a shorter cycle of clinical trials, while plasma isolated from COVID-19 recovered patients can be a good source of neutralizing antibody to provide passive immunity. In this review, we provide in-depth analysis on these two approaches currently opted all around the world to treat COVID-19 patients. For this, we used "Boolean Operators" such as AND, OR & NOT to search relevant research articles/reviews from the PUBMED for the repurposed drugs and the convalescent plasma in the COVID-19 treatment. The repurposed drugs like Chloroquine and Hydroxychloroquine, Tenofovir, Remdesivir, Ribavirin, Darunavir, Oseltamivir, Arbidol (Umifenovir), Favipiravir, Anakinra, and Baricitinib are already being used in clinical trials to treat the COVID-19 patients. These drugs have been approved for a different indication and belong to a diverse category such as anti-malarial/anti-parasitic, anti-retroviral/anti-viral, anti-cancer, or against rheumatoid arthritis. Although, the vaccine would be an ideal option for providing active immunity against the SARS-CoV-2, but considering the current situation, drug repurposing and convalescent plasma therapy and repurposed drugs are the most viable option against SARS-CoV-2.
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Affiliation(s)
- Pravindra Kumar
- School of Life & Allied Health Sciences, The Glocal University, Saharanpur, UP, India
| | - Ashok Kumar Sah
- Department of Medical Laboratory Technology, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, India
| | - Greesham Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, 122413, India
| | - Anjali Kashyap
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Avantika Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, 122413, India
| | - Rashmi Rao
- School of Life & Allied Health Sciences, The Glocal University, Saharanpur, UP, India
| | - Prabhu C Mishra
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, 122413, India
| | - Koustav Mallick
- National Liver Disease Biobank, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Amjad Husain
- Centre for Science & Society, Indian Institute of Science Education and Research, Bhopal, India
- Innovation and Incubation Centre for Entrepreneurship (IICE), Indian Institute of Science Education and Research, Bhopal, India
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, 122413, India.
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17
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Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies. Cell Mol Life Sci 2020; 78:1501-1522. [PMID: 32623480 PMCID: PMC7334636 DOI: 10.1007/s00018-020-03580-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/10/2020] [Accepted: 06/22/2020] [Indexed: 12/19/2022]
Abstract
The recent severe acute respiratory syndrome, known as Coronavirus Disease 2019 (COVID-19) has spread so much rapidly and severely to induce World Health Organization (WHO) to declare a state of emergency over the new coronavirus SARS-CoV-2 pandemic. While several countries have chosen the almost complete lock-down for slowing down SARS-CoV-2 spread, the scientific community is called to respond to the devastating outbreak by identifying new tools for diagnosis and treatment of the dangerous COVID-19. With this aim, we performed an in silico comparative modeling analysis, which allows gaining new insights into the main conformational changes occurring in the SARS-CoV-2 spike protein, at the level of the receptor-binding domain (RBD), along interactions with human cells angiotensin-converting enzyme 2 (ACE2) receptor, that favor human cell invasion. Furthermore, our analysis provides (1) an ideal pipeline to identify already characterized antibodies that might target SARS-CoV-2 spike RBD, aiming to prevent interactions with the human ACE2, and (2) instructions for building new possible neutralizing antibodies, according to chemical/physical space restraints and complementary determining regions (CDR) mutagenesis of the identified existing antibodies. The proposed antibodies show in silico high affinity for SARS-CoV-2 spike RBD and can be used as reference antibodies also for building new high-affinity antibodies against present and future coronaviruses able to invade human cells through interactions of their spike proteins with the human ACE2. More in general, our analysis provides indications for the set-up of the right biological molecular context for investigating spike RBD–ACE2 interactions for the development of new vaccines, diagnostic kits, and other treatments based on the targeting of SARS-CoV-2 spike protein.
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18
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Tan D, Hansen MF, de Carvalho LN, Røder HL, Burmølle M, Middelboe M, Svenningsen SL. High cell densities favor lysogeny: induction of an H20 prophage is repressed by quorum sensing and enhances biofilm formation in Vibrio anguillarum. THE ISME JOURNAL 2020; 14:1731-1742. [PMID: 32269377 PMCID: PMC7305317 DOI: 10.1038/s41396-020-0641-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 11/09/2022]
Abstract
Temperate ϕH20-like phages are repeatedly identified at geographically distinct areas as free phage particles or as prophages of the fish pathogen Vibrio anguillarum. We studied mutants of a lysogenic isolate of V. anguillarum locked in the quorum-sensing regulatory modes of low (ΔvanT) and high (ΔvanO) cell densities by in-frame deletion of key regulators of the quorum-sensing pathway. Remarkably, we find that induction of the H20-like prophage is controlled by the quorum-sensing state of the host, with an eightfold increase in phage particles per cell in high-cell-density cultures of the quorum-sensing-deficient ΔvanT mutant. Comparative studies with prophage-free strains show that biofilm formation is promoted at low cell density and that the H20-like prophage stimulates this behavior. In contrast, the high-cell-density state is associated with reduced prophage induction, increased proteolytic activity, and repression of biofilm. The proteolytic activity may dually function to disperse the biofilm and as a quorum-sensing-mediated antiphage strategy. We demonstrate an intertwined regulation of phage-host interactions and biofilm formation, which is orchestrated by host quorum-sensing signaling, suggesting that increased lysogeny at high cell density is not solely a strategy for phages to piggy-back the successful bacterial hosts but is also a host strategy evolved to take control of the lysis-lysogeny switch to promote host fitness.
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Affiliation(s)
- Demeng Tan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Dalian SEM Bio-Engineering Technology Co. Ltd, Dalian, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mads Frederik Hansen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | | | - Mette Burmølle
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mathias Middelboe
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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