The fish pathogen Flavobacterium columnare represents four distinct

Chemotaxonomic, MALDI-TOF characterization and ANI/GGDC calculations afforded differentiation between the genetic groups, indicating each group is a discrete species. Herein, the names F. covae sp. nov. (AL-02-36T), F. davisii sp. nov. (90-106T), and F. oreochromis sp. nov. (Costa Rica 04-02-TNT) are proposed to represent genetic groups 2, 3, and 4, respectively.

[1]  B. LaFrentz,et al.  Genetic characterization of Flavobacterium columnare isolates from the Pacific Northwest, USA. , 2021, Diseases of aquatic organisms.

[2]  B. LaFrentz,et al.  Flavobacterium inkyongense isolated from ornamental cichlids. , 2019, Journal of fish diseases.

[3]  B. LaFrentz,et al.  Multiplex PCR for genotyping Flavobacterium columnare. , 2019, Journal of fish diseases.

[4]  M. A. Peterman,et al.  Direct Economic Impact of Fish Diseases on the East Mississippi Catfish Industry , 2019, North American Journal of Aquaculture.

[5]  M. Barták,et al.  Flavobacterium circumlabens sp. nov. and Flavobacterium cupreum sp. nov., two psychrotrophic species isolated from Antarctic environmental samples. , 2019, Systematic and applied microbiology.

[6]  Soon-Wo Kwon,et al.  Flavobacterium effusum sp. nov., isolated from a freshwater river. , 2018, International journal of systematic and evolutionary microbiology.

[7]  P. Švec,et al.  Flavobacterium chryseum sp. nov. and Flavobacterium psychroterrae sp. nov., novel environmental bacteria isolated from Antarctica. , 2018, International journal of systematic and evolutionary microbiology.

[8]  O. Chesneau,et al.  Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar III Strain PH-97028 (=CIP 109753) , 2018, Genome Announcements.

[9]  Yi-Xuan Zhang,et al.  Flavobacterium artemisiae sp. nov., isolated from the rhizosphere of Artemisia annua L. and emended descriptions of Flavobacterium compostarboris and Flavobacterium procerum. , 2018, International journal of systematic and evolutionary microbiology.

[10]  M. Liles,et al.  Identification of Four Distinct Phylogenetic Groups in Flavobacterium columnare With Fish Host Associations , 2018, Front. Microbiol..

[11]  Wen‐Ming Chen,et al.  Flavobacterium fluviatile sp. nov., isolated from a freshwater creek. , 2018, International journal of systematic and evolutionary microbiology.

[12]  Ji-Hye Bu,et al.  Flavobacterium foetidum sp. nov., isolated from ginseng soil. , 2018, International journal of systematic and evolutionary microbiology.

[13]  A. Phillippy,et al.  High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries , 2017, Nature Communications.

[14]  T. Welch,et al.  Comparative Phenotypic and Genotypic Analysis of Edwardsiella Isolates from Different Hosts and Geographic Origins, with Emphasis on Isolates Formerly Classified as E. tarda, and Evaluation of Diagnostic Methods , 2017, Journal of Clinical Microbiology.

[15]  C. Rodkhum,et al.  Comparative genome analysis of fish pathogen Flavobacterium columnare reveals extensive sequence diversity within the species. , 2017, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[16]  C. Rodkhum,et al.  Optimized reverse primer for 16S-RFLP analysis and genomovar assignment of Flavobacterium columnare. , 2017, Journal of fish diseases.

[17]  A. Karsi,et al.  Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes , 2017, Front. Microbiol..

[18]  S. Koren,et al.  Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.

[19]  P. Gaunt,et al.  Development of new G media for culture of Flavobacterium columnare and comparison with other media. , 2016 .

[20]  B. LaFrentz,et al.  Virulence of Flavobacterium columnare genomovars in rainbow trout Oncorhynchus mykiss. , 2016, Diseases of aquatic organisms.

[21]  A. Karsi,et al.  Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar II Strain 94-081 , 2016, Genome Announcements.

[22]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[23]  C. Gieseker,et al.  Development of Similar Broth Microdilution Methods to Determine the Antimicrobial Susceptibility of Flavobacterium columnare and F. psychrophilum. , 2016, Journal of aquatic animal health.

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

[25]  V. Mikhailov,et al.  Flavobacterium maris sp. nov. isolated from shallow sediments of the Sea of Japan , 2015, Archives of Microbiology.

[26]  Wenjun Li,et al.  Flavobacterium notoginsengisoli sp. nov., isolated from the rhizosphere of Panax notoginseng , 2015, Antonie van Leeuwenhoek.

[27]  M. Faisal,et al.  Emerging flavobacterial infections in fish: A review , 2014, Journal of advanced research.

[28]  S. J. Scott,et al.  Flavobacterium columnare: an important contributing factor to fish die-offs in southern lakes of Saskatchewan, Canada , 2014, Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc.

[29]  T. Welch,et al.  Flavobacterium branchiophilum and F. succinicans associated with bacterial gill disease in rainbow trout Oncorhynchus mykiss (Walbaum) in water recirculation aquaculture systems , 2014, Journal of fish diseases.

[30]  J. Chun,et al.  Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. , 2014, International journal of systematic and evolutionary microbiology.

[31]  M. Faisal,et al.  Flavobacterium spartansii sp. nov., a pathogen of fishes, and emended descriptions of Flavobacterium aquidurense and Flavobacterium araucananum. , 2014, International journal of systematic and evolutionary microbiology.

[32]  E. Moore,et al.  Flavobacterium tructae sp. nov. and Flavobacterium piscis sp. nov., isolated from farmed rainbow trout (Oncorhynchus mykiss). , 2014, International journal of systematic and evolutionary microbiology.

[33]  E. Moore,et al.  Characterization of flavobacteria possibly associated with fish and fish farm environment. Description of three novel Flavobacterium species: Flavobacterium collinsii sp. nov., Flavobacterium branchiarum sp. nov., and Flavobacterium branchiicola sp. nov. , 2013 .

[34]  J. Chun,et al.  Flavobacterium limnosediminis sp. nov., isolated from sediment of a freshwater lake. , 2013, International journal of systematic and evolutionary microbiology.

[35]  E. Moore,et al.  Flavobacterium plurextorum sp. nov. Isolated from Farmed Rainbow Trout (Oncorhynchus mykiss) , 2013, PloS one.

[36]  Xiuzhu Dong,et al.  Flavobacterium noncentrifugens sp. nov., a psychrotolerant bacterium isolated from glacier meltwater. , 2013, International journal of systematic and evolutionary microbiology.

[37]  F. Haesebrouck,et al.  Columnaris disease in fish: a review with emphasis on bacterium-host interactions , 2013, Veterinary Research.

[38]  Alexander F. Auch,et al.  Genome sequence-based species delimitation with confidence intervals and improved distance functions , 2013, BMC Bioinformatics.

[39]  E. Kanaya,et al.  Flavobacterium compostarboris sp. nov., isolated from leaf-and-branch compost, and emended descriptions of Flavobacterium hercynium, Flavobacterium resistens and Flavobacterium johnsoniae. , 2012, International journal of systematic and evolutionary microbiology.

[40]  P. Kämpfer,et al.  Flavobacterium chilense sp. nov. and Flavobacterium araucananum sp. nov., isolated from farmed salmonid fish. , 2012, International journal of systematic and evolutionary microbiology.

[41]  J. Chun,et al.  Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. , 2012, International journal of systematic and evolutionary microbiology.

[42]  E. Moore,et al.  Flavobacterium oncorhynchi sp. nov., a new species isolated from rainbow trout (Oncorhynchus mykiss). , 2012, Systematic and applied microbiology.

[43]  H. S. Davis A New Bacterial Disease of Fresh-Water Fishes , 2011 .

[44]  A. Willems,et al.  The gyrB gene is a useful phylogenetic marker for exploring the diversity of Flavobacterium strains isolated from terrestrial and aquatic habitats in Antarctica. , 2011, FEMS microbiology letters.

[45]  E. Stackebrandt,et al.  Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet. , 2009, International journal of systematic and evolutionary microbiology.

[46]  P. Klesius,et al.  Development of a culture independent method to characterize the chemotactic response of Flavobacterium columnare to fish mucus. , 2009, Journal of microbiological methods.

[47]  P. Klesius,et al.  Flavobacterium columnare genomovar influences mortality in channel catfish (Ictalurus punctatus). , 2008, Veterinary microbiology.

[48]  T. Oh,et al.  Flavobacterium soli sp. nov., isolated from soil. , 2006, International journal of systematic and evolutionary microbiology.

[49]  L. Caslake,et al.  Genetic diversity of Flavobacterium columnare isolated from fish collected from warm and cold water. , 2006, Journal of fish diseases.

[50]  Joseph S. Meyer,et al.  Survival of Lost River Suckers (Deltistes luxatus) Challenged with Flavobacterium columnare During Exposure to Sublethal Ammonia Concentrations at pH 9.5 , 2006, Archives of environmental contamination and toxicology.

[51]  K. Soda,et al.  Flavobacterium frigidimaris sp. nov., isolated from Antarctic seawater. , 2005, Systematic and applied microbiology.

[52]  J. Mergaert,et al.  Flavobacterium gelidilacus sp. nov., isolated from microbial mats in Antarctic lakes. , 2003, International journal of systematic and evolutionary microbiology.

[53]  L. Khoo,et al.  The Epidemiology of Bacterial Diseases in Food-Size Channel Catfish. , 2002, Journal of aquatic animal health.

[54]  L. Khoo,et al.  The Epidemiology of Bacterial Diseases in Food-Size Channel Catfish. , 2002, Journal of aquatic animal health.

[55]  Y. Nakagawa,et al.  Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. , 2002, International journal of systematic and evolutionary microbiology.

[56]  Triyanto,et al.  Genotypic Diversity of Strains of Flavobacterium columnare from Diseased Fishes , 1999 .

[57]  MD Penney,et al.  Quality Management for Chemical Safety, Environmental Health Criteria No. 141 , 1993 .

[58]  M. Nei,et al.  Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. , 1993, Molecular biology and evolution.

[59]  B. Tindall A comparative study of the lipid composition of Halobacterium saccharovorum from various sources , 1990 .

[60]  P. Grimont,et al.  Deoxyribonucleic Acid Relatedness and Phenotypic Characterization of Flexibacter columnaris sp. nov., nom. rev., Flexibacter psychrophilus sp. nov., nom. rev., and Flexibacter maritimus Wakabayashi, Hikida, and Masumura 1986 , 1989 .

[61]  J. Rohovec,et al.  Comparison of Gliding Bacteria Isolated from Fish in North America and Other Areas of the Pacific Rim , 1988 .

[62]  Lawrence G. Wayne,et al.  International Committee on Systematic Bacteriology: Announcement of the Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics , 1988 .

[63]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[64]  M. Kocur,et al.  New medium for detection of esterase and gelatinase activity. , 1984, Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectious diseases, virology, parasitology.

[65]  V. Kurup,et al.  Use of casein, tyrosine, and hypoxanthine in the identification of nonfermentative gram-negative bacilli , 1979, Medical Microbiology and Immunology.

[66]  W. Strohl,et al.  Cytophaga aquatilis sp. nov., a Facultative Anaerobe Isolated from the Gills of Freshwater Fish , 1978 .

[67]  T. R. Oberhofer,et al.  Acetamide agar for differentiation of nonfermentative bacteria. , 1974, Applied microbiology.

[68]  J. J. Owens The egg yolk reaction produced by several species of bacteria. , 1974, The Journal of applied bacteriology.

[69]  W. J. Dyer,et al.  A rapid method of total lipid extraction and purification. , 1959, Canadian journal of biochemistry and physiology.

[70]  E. Leifson,et al.  THE TAXONOMIC SIGNIFICANCE OF FERMENTATIVE VERSUS OXIDATIVE METABOLISM OF CARBOHYDRATES BY VARIOUS GRAM NEGATIVE BACTERIA , 1953, Journal of bacteriology.

[71]  W. B. Christensen,et al.  Urea Decomposition as a Means of Differentiating Proteus and Paracolon Cultures from Each Other and from Salmonella and Shigella Types , 1946, Journal of bacteriology.

[72]  L. Garnjobst Cytophaga columnaris (Davis) in Pure Culture: A Myxobacterium Pathogenic to Fish , 1945, Journal of bacteriology.

[73]  R. R. Rucker,et al.  Pathogenic Myxobacteria , 1944 .

[74]  M. McBride The Family Flavobacteriaceae , 2014 .

[75]  E. Delong,et al.  The Prokaryotes : Other Major Lineages of Bacteria and The Archaea , 2014 .

[76]  Wonyong Kim,et al.  Flavobacterium ponti sp. nov., isolated from seawater. , 2011, International journal of systematic and evolutionary microbiology.

[77]  A. Oskooi Molecular Evolution and Phylogenetics , 2008 .

[78]  B. Tindall,et al.  Phenotypic Characterization and the Principles of Comparative Systematics , 2007 .

[79]  T. Beveridge,et al.  Methods for general and molecular microbiology , 2007 .

[80]  P. Vandamme,et al.  DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. , 2007, International journal of systematic and evolutionary microbiology.

[81]  P. Dawyndt,et al.  Diversity of 746 heterotrophic bacteria isolated from microbial mats from ten Antarctic lakes. , 2002, Systematic and applied microbiology.

[82]  P. Vandamme,et al.  Cutting a gordian knot: Emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom nov (basonym, Cytophaga aquatilis Strohl and Tait 1978). , 1996 .

[83]  G. Barrow,et al.  Cowan and Steel's Manual for the identification of medical bacteria: Index , 1993 .

[84]  B. Tindall Lipid composition of Halobacterium lacusprofundi , 1990 .

[85]  J. Bernardet 'Flexibacter columnaris': first description in France and comparison with bacterial strains from other origins. , 1989 .

[86]  S. T. Cowan Bergey's Manual of Determinative Bacteriology , 1948, Nature.