TY - JOUR
T1 - The fish pathogen Flavobacterium columnare represents four distinct species
T2 - Flavobacterium columnare, Flavobacterium covae sp. nov., Flavobacterium davisii sp. nov. and Flavobacterium oreochromis sp. nov., and emended description of Flavobacterium columnare
AU - LaFrentz, Benjamin R.
AU - Králová, Stanislava
AU - Burbick, Claire R.
AU - Alexander, Trevor L.
AU - Phillips, Conner W.
AU - Griffin, Matt J.
AU - Waldbieser, Geoffrey C.
AU - García, Julio C.
AU - de Alexandre Sebastião, Fernanda
AU - Soto, Esteban
AU - Loch, Thomas P.
AU - Liles, Mark R.
AU - Snekvik, Kevin R.
N1 - Funding Information:
The authors thank Dr. Johnny Shelley and Alison Aceves of USDA-ARS, Cynthia Ware of Mississippi State University, and Beth Pepper of the Washington Animal Disease Diagnostic Laboratory for technical support, and Dr. Michael Miller of the Auburn University Research Instrumentation Facility for assistance and technical support for electron microscopy. The authors thank Prof. Bernhard Schink (University of Konstanz, Germany) for the name correction. The authors acknowledge isolate contributions from Bill Hemstreet (Auburn University), Dr. Jason Evenhuis (USDA-ARS), Dr. Mark Lawrence (Mississippi State University), and Bradley Farmer (USDA-ARS). The authors would also like to thank Dr. Jean-Fran?ois Bernardet and Dr. Eric Duchaud (Universit? Paris-Saclay, INRAE, MaIAGE, France) for critical review of the manuscript. This research was supported by USDA-ARS CRIS Project No. 6010-32000-027-00-D, Integrated Research to Improve Aquatic Animal Health in Warmwater Aquaculture. Isolates TI2063, TI1690, TI2056, and TI1371 were transferred to USDA-ARS through Material Transfer Research Agreement Number 58-6010-6-006-F. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the United States Department of Agriculture.
Funding Information:
The authors thank Dr. Johnny Shelley and Alison Aceves of USDA-ARS, Cynthia Ware of Mississippi State University, and Beth Pepper of the Washington Animal Disease Diagnostic Laboratory for technical support, and Dr. Michael Miller of the Auburn University Research Instrumentation Facility for assistance and technical support for electron microscopy. The authors thank Prof. Bernhard Schink (University of Konstanz, Germany) for the name correction. The authors acknowledge isolate contributions from Bill Hemstreet (Auburn University), Dr. Jason Evenhuis (USDA-ARS), Dr. Mark Lawrence (Mississippi State University), and Bradley Farmer (USDA-ARS). The authors would also like to thank Dr. Jean-François Bernardet and Dr. Eric Duchaud (Université Paris-Saclay, INRAE, MaIAGE, France) for critical review of the manuscript. This research was supported by USDA-ARS CRIS Project No. 6010-32000-027-00-D, Integrated Research to Improve Aquatic Animal Health in Warmwater Aquaculture. Isolates TI2063, TI1690, TI2056, and TI1371 were transferred to USDA-ARS through Material Transfer Research Agreement Number 58-6010-6-006-F. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the United States Department of Agriculture.
Publisher Copyright:
© 2022
PY - 2022/4
Y1 - 2022/4
N2 - Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish and four discrete genetic groups exist within the species, suggesting that the species designation requires revision. The present study determined the taxonomic status of the four genetic groups of F. columnare using polyphasic and phylogenomic approaches and included five representative isolates from each genetic group (including type strain ATCC 23463T; genetic group 1). 16S rRNA gene sequence analysis revealed genetic group 2 isolate AL-02-36T, genetic group 3 isolate 90-106T, and genetic group 4 isolate Costa Rica 04-02-TNT shared less than <98.8 % sequence identity to F. columnare ATCC 23463T. Phylogenetic analyses of 16S rRNA and gyrB genes using different methodologies demonstrated the four genetic groups formed well-supported and distinct clades within the genus Flavobacterium. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) values between F. columnare ATCC 23463T, genetic group 2 isolate AL-02-36T, genetic group 3 isolate 90-106T, and genetic group 4 isolate Costa Rica 04-02-TNT were less than 90.84% and 42.7%, respectively. Biochemical and physiological characteristics were similar among the four genetic groups; however, quantitative differences in fatty acid profiles were detected and MALDI-TOF analyses demonstrated numerous distinguishing peaks unique to each genetic group. 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.
AB - Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish and four discrete genetic groups exist within the species, suggesting that the species designation requires revision. The present study determined the taxonomic status of the four genetic groups of F. columnare using polyphasic and phylogenomic approaches and included five representative isolates from each genetic group (including type strain ATCC 23463T; genetic group 1). 16S rRNA gene sequence analysis revealed genetic group 2 isolate AL-02-36T, genetic group 3 isolate 90-106T, and genetic group 4 isolate Costa Rica 04-02-TNT shared less than <98.8 % sequence identity to F. columnare ATCC 23463T. Phylogenetic analyses of 16S rRNA and gyrB genes using different methodologies demonstrated the four genetic groups formed well-supported and distinct clades within the genus Flavobacterium. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) values between F. columnare ATCC 23463T, genetic group 2 isolate AL-02-36T, genetic group 3 isolate 90-106T, and genetic group 4 isolate Costa Rica 04-02-TNT were less than 90.84% and 42.7%, respectively. Biochemical and physiological characteristics were similar among the four genetic groups; however, quantitative differences in fatty acid profiles were detected and MALDI-TOF analyses demonstrated numerous distinguishing peaks unique to each genetic group. 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.
KW - Columnaris disease
KW - Genetic groups
KW - MALDI-TOF
KW - Polyphasic
KW - Taxonomy
UR - http://www.scopus.com/inward/record.url?scp=85122518462&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85122518462&partnerID=8YFLogxK
U2 - 10.1016/j.syapm.2021.126293
DO - 10.1016/j.syapm.2021.126293
M3 - Article
C2 - 35026686
AN - SCOPUS:85122518462
VL - 45
JO - Systematic and Applied Microbiology
JF - Systematic and Applied Microbiology
SN - 0723-2020
IS - 2
M1 - 126293
ER -