Isolation and characterization of a novel Tenacibaculum species and a corresponding bacteriophage from a Mediterranean fish hatchery: Description of Tenacibaculum larymnensis sp. nov. and Tenacibaculum phage Larrie

Tenacibaculum larymnensis sp. nov., a novel species of the Tenacibaculum genus was isolated from a commercial fish hatchery in Greece. The novel species is phylogenetically close to T. discolor and was biochemically and genetically characterized. The genome of T. larymnensis has 3.66 Mbps length, 31.83% GC content and the genomic analysis demonstrated that it harbors a wide enzymatic repertoire suggestive of increased degrading capacity but also several virulence factors including hemolysins, secretion systems, transporters, siderophores, pili and extracellular proteins. Using the novel strain, a virulent bacteriophage designated as Tenacibaculum phage Larrie was isolated and characterized. Larrie is a novel Siphovirus with relatively large genome, 77.5 kbps with 111 ORFs, a GC content of 33.7% and an exclusively lytic lifestyle. The new phage-host system can serve as an efficient model to study microbial interactions in the aquatic environment which contribute to the nutrient cycling.

[1]  Franklin L. Nobrega,et al.  Defence systems provide synergistic anti-phage activity in E. coli , 2022, bioRxiv.

[2]  E. Rocha,et al.  IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella , 2022, bioRxiv.

[3]  P. J. Kranzusch,et al.  CBASS phage defense and evolution of antiviral nucleotide signaling. , 2022, Current opinion in immunology.

[4]  M. Touchon,et al.  Systematic and quantitative view of the antiviral arsenal of prokaryotes , 2021, Nature Communications.

[5]  A. Nylund,et al.  Phylogenetic analyses of Norwegian Tenacibaculum strains confirm high bacterial diversity and suggest circulation of ubiquitous virulent strains , 2021, PloS one.

[6]  E. Westra,et al.  Interactions between bacterial and phage communities in natural environments , 2021, Nature Reviews Microbiology.

[7]  R. Avendaño‐Herrera,et al.  Comparison between genome sequences of Chilean Tenacibaculum dicentrarchi isolated from red conger eel (Genypterus chilensis) and Atlantic salmon (Salmo salar) focusing on bacterial virulence determinants. , 2021, Journal of fish diseases.

[8]  S. Iyoda,et al.  Diversity of the Tellurite Resistance Gene Operon in Escherichia coli , 2021, Frontiers in Microbiology.

[9]  Alexander M. Kloosterman,et al.  antiSMASH 6.0: improving cluster detection and comparison capabilities , 2021, Nucleic Acids Res..

[10]  B. Macey,et al.  Bacterial microbiome of dusky kob Argyrosomus japonicus eggs and rearing water and the bacteriostatic effect of selected disinfectants , 2021 .

[11]  P. Bork,et al.  Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation , 2021, Nucleic Acids Res..

[12]  Hanna Koch,et al.  Sweet spheres: Succession and CAZyme expression of marine bacterial communities colonising a mix of alginate and pectin particles. , 2021, Environmental microbiology.

[13]  C. Magalhães,et al.  Microbial community dynamics in a hatchery recirculating aquaculture system (RAS) of sole (Solea senegalensis) , 2021 .

[14]  Thomas M. Keane,et al.  Twelve years of SAMtools and BCFtools , 2020, GigaScience.

[15]  Narmada Thanki,et al.  RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation , 2020, Nucleic Acids Res..

[16]  M. Fioravanti,et al.  Best therapeutic practices for the use of antibacterial agents in finfish aquaculture: a particular view on European seabass ( Dicentrarchus labrax ) and gilthead seabream ( Sparus aurata ) in Mediterranean aquaculture , 2020 .

[17]  P. Katharios,et al.  Biological and Genomic Characterization of a Novel Jumbo Bacteriophage, vB_VhaM_pir03 with Broad Host Lytic Activity against Vibrio harveyi , 2020, Pathogens.

[18]  J. Lumsden,et al.  Advancements in Characterizing Tenacibaculum Infections in Canada , 2020, Pathogens.

[19]  K. Lagesen,et al.  Tenacibaculum piscium sp. nov., isolated from skin ulcers of sea-farmed fish, and description of Tenacibaculum finnmarkense sp. nov. with subdivision into genomovars finnmarkense and ulcerans. , 2020, International journal of systematic and evolutionary microbiology.

[20]  M. Parker,et al.  A Key Motif in the Cholesterol-Dependent Cytolysins Reveals a Large Family of Related Proteins , 2020, mBio.

[21]  R. Avendaño‐Herrera,et al.  New salmonid hosts for Tenacibaculum species: Expansion of tenacibaculosis in Chilean aquaculture. , 2020, Journal of fish diseases.

[22]  S. McLellan,et al.  Microbial Communities Associated with Farmed Genypterus chilensis: Detection in Water Prior to Bacterial Outbreaks Using Culturing and High-Throughput Sequencing , 2020, Animals : an open access journal from MDPI.

[23]  C. Wilke,et al.  BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains , 2020, bioRxiv.

[24]  H. Smidt,et al.  Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis , 2020, BMC Genomics.

[25]  Narmada Thanki,et al.  CDD/SPARCLE: the conserved domain database in 2020 , 2019, Nucleic Acids Res..

[26]  Rick L. Stevens,et al.  The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities , 2019, Nucleic Acids Res..

[27]  T. Nakai,et al.  A novel jumbo Tenacibaculum maritimum lytic phage with head-fiber-like appendages , 2019, Archives of Virology.

[28]  M. Middelboe,et al.  Big Impact of the Tiny: Bacteriophage-Bacteria Interactions in Biofilms. , 2019, Trends in microbiology.

[29]  H. Dahle,et al.  Microbial Communities in a Flow-Through Fish Farm for Lumpfish (Cyclopterus lumpus L.) During Healthy Rearing Conditions , 2019, Front. Microbiol..

[30]  E. Laanto,et al.  Aquaculture as a source of empirical evidence for coevolution between CRISPR-Cas and phage , 2019, Philosophical Transactions of the Royal Society B.

[31]  Jeremy J. Barr,et al.  Phage Therapy in the Postantibiotic Era , 2019, Clinical Microbiology Reviews.

[32]  Silvio C. E. Tosatto,et al.  InterPro in 2019: improving coverage, classification and access to protein sequence annotations , 2018, Nucleic Acids Res..

[33]  A. Phillippy,et al.  High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries , 2018, Nature Communications.

[34]  Keith A Jolley,et al.  Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications , 2018, Wellcome open research.

[35]  Sudhir Kumar,et al.  MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. , 2018, Molecular biology and evolution.

[36]  Marius van den Beek,et al.  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update , 2018, Nucleic Acids Res..

[37]  Zhenglu Yang,et al.  dbCAN2: a meta server for automated carbohydrate-active enzyme annotation , 2018, Nucleic Acids Res..

[38]  A. Nylund,et al.  Experimental induction of mouthrot in Atlantic salmon smolts using Tenacibaculum maritimum from Western Canada. , 2018, Journal of fish diseases.

[39]  M. Faisal,et al.  Flavobacteria colonizing the early life stages of hatchery-incubated Chinook salmon Oncorhynchus tshawytscha (Walbaum 1792) are markedly diverse. , 2018, Journal of fish diseases.

[40]  Rotem Sorek,et al.  Systematic discovery of antiphage defense systems in the microbial pangenome , 2018, Science.

[41]  M. Middelboe,et al.  Bacteriophage Interactions with Marine Pathogenic Vibrios: Implications for Phage Therapy , 2018, Antibiotics.

[42]  G. Achaz,et al.  Comparative Genomics of Tenacibaculum dicentrarchi and “Tenacibaculum finnmarkense” Highlights Intricate Evolution of Fish-Pathogenic Species , 2018, Genome biology and evolution.

[43]  Jian Wang,et al.  SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data , 2017, GigaScience.

[44]  M. Middelboe,et al.  Isolation and characterization of a N4-like lytic bacteriophage infecting Vibrio splendidus, a pathogen of fish and bivalves , 2017, PloS one.

[45]  Fernando de la Cruz,et al.  PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes , 2017, Bioinform..

[46]  G. Michel,et al.  The Complete Genome Sequence of the Fish Pathogen Tenacibaculum maritimum Provides Insights into Virulence Mechanisms , 2017, Front. Microbiol..

[47]  Takashi Yoshida,et al.  ViPTree: the viral proteomic tree server , 2017, Bioinform..

[48]  H. Schreier,et al.  The Rising Tide of Antimicrobial Resistance in Aquaculture: Sources, Sinks and Solutions , 2017, Marine drugs.

[49]  Matthew R. Laird,et al.  IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets , 2017, Nucleic Acids Res..

[50]  Alejandro A. Schäffer,et al.  Virus Variation Resource – improved response to emergent viral outbreaks , 2016, Nucleic Acids Res..

[51]  Ryan R. Wick,et al.  Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads , 2016, bioRxiv.

[52]  A. Nylund,et al.  First isolation, identification and characterisation of Tenacibaculum maritimum in Norway, isolated from diseased farmed sea lice cleaner fish Cyclopterus lumpus L , 2016 .

[53]  David S. Wishart,et al.  PHASTER: a better, faster version of the PHAST phage search tool , 2016, Nucleic Acids Res..

[54]  K. Konstantinidis,et al.  The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes , 2016 .

[55]  M. Kanehisa,et al.  BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences. , 2016, Journal of molecular biology.

[56]  J. Chun,et al.  OrthoANI: An improved algorithm and software for calculating average nucleotide identity. , 2016, International journal of systematic and evolutionary microbiology.

[57]  A. Otero,et al.  Aii20J, a wide-spectrum thermostable N-acylhomoserine lactonase from the marine bacterium Tenacibaculum sp. 20J, can quench AHL-mediated acid resistance in Escherichia coli , 2015, Applied Microbiology and Biotechnology.

[58]  Justin Zobel,et al.  Bandage: interactive visualization of de novo genome assemblies , 2015, bioRxiv.

[59]  Fangfang Xia,et al.  RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes , 2015, Scientific Reports.

[60]  R. E. Yardımcı,et al.  Isolation and Identification of Tenacibaculum maritimum, the Causative Agent of Tenacibaculosis in Farmed Sea Bass (Dicentrarchus labrax) on the Aegean Sea Coast of Turkey , 2015 .

[61]  Christina A. Cuomo,et al.  Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement , 2014, PloS one.

[62]  Hervé Ménager,et al.  MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems , 2014, PloS one.

[63]  B. Magariños,et al.  In vitro quenching of fish pathogen Edwardsiella tarda AHL production using marine bacterium Tenacibaculum sp. strain 20J cell extracts. , 2014, Diseases of aquatic organisms.

[64]  Mette Voldby Larsen,et al.  Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences , 2014, Bacteriophage.

[65]  M. Cunliffe,et al.  Seasonal microbial community dynamics correlate with phytoplankton-derived polysaccharides in surface coastal waters , 2013, The ISME Journal.

[66]  Manesh Shah,et al.  Twelve previously unknown phage genera are ubiquitous in global oceans , 2013, Proceedings of the National Academy of Sciences.

[67]  Alexey A. Gurevich,et al.  QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..

[68]  M. McBride,et al.  Gliding Motility and Por Secretion System Genes Are Widespread among Members of the Phylum Bacteroidetes , 2012, Journal of bacteriology.

[69]  R. Tweten,et al.  Identification and Characterization of the First Cholesterol-Dependent Cytolysins from Gram-Negative Bacteria , 2012, Infection and Immunity.

[70]  Y. Santos,et al.  Tenacibaculum dicentrarchi sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from European sea bass. , 2012, International journal of systematic and evolutionary microbiology.

[71]  Mya Breitbart,et al.  Marine viruses: truth or dare. , 2012, Annual review of marine science.

[72]  N. Perna,et al.  progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement , 2010, PloS one.

[73]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[74]  António Correia,et al.  INTEGRALL: a database and search engine for integrons, integrases and gene cassettes , 2009, Bioinform..

[75]  E. Kutter Phage host range and efficiency of plating. , 2009, Methods in molecular biology.

[76]  A. Karagouni,et al.  Prevalence of tetracycline resistance genes in Greek seawater habitats , 2008, The Journal of Microbiology.

[77]  F. Pazos,et al.  Fatty acid analysis as a chemotaxonomic tool for taxonomic and epidemiological characterization of four fish pathogenic Tenacibaculum species , 2008, Letters in applied microbiology.

[78]  Y. Santos,et al.  Tenacibaculum soleae sp. nov., isolated from diseased sole (Solea senegalensis Kaup). , 2008, International journal of systematic and evolutionary microbiology.

[79]  Y. Santos,et al.  Tenacibaculum discolor sp. nov. and Tenacibaculum gallaicum sp. nov., isolated from sole (Solea senegalensis) and turbot (Psetta maxima) culture systems. , 2008, International journal of systematic and evolutionary microbiology.

[80]  A. E. Toranzo,et al.  Evolution of drug resistance and minimum inhibitory concentration to enrofloxacin in Tenacibaculum maritimum strains isolated in fish farms , 2008, Aquaculture International.

[81]  Steven Salzberg,et al.  Identifying bacterial genes and endosymbiont DNA with Glimmer , 2007, Bioinform..

[82]  A. E. Toranzo,et al.  Tenacibaculosis infection in marine fish caused by Tenacibaculum maritimum: a review. , 2006, Diseases of aquatic organisms.

[83]  Jun Yu,et al.  VFDB: a reference database for bacterial virulence factors , 2004, Nucleic Acids Res..

[84]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[85]  Dean Laslett,et al.  ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. , 2004, Nucleic acids research.

[86]  B Marshall,et al.  Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource , 2004, Nucleic Acids Res..

[87]  V. Rao,et al.  Sequence analysis of bacteriophage T4 DNA packaging/terminase genes 16 and 17 reveals a common ATPase center in the large subunit of viral terminases. , 2002, Nucleic acids research.

[88]  S. Harayama,et al.  Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov. , 2001, International journal of systematic and evolutionary microbiology.

[89]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[90]  Michael W Parker,et al.  Structure of a Cholesterol-Binding, Thiol-Activated Cytolysin and a Model of Its Membrane Form , 1997, Cell.

[91]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[92]  T. Devine,et al.  Fatty Acids, Antibiotic Resistance, and Deoxyribonucleic Acid Homology Groups of Bradyrhizobium japonicum , 1988 .

[93]  L. Miller Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids , 1982, Journal of clinical microbiology.