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Int J Syst Bacteriol 46 (1996), 128-148; DOI 10.1099/00207713-46-1-128
© 1996 Society for General Microbiology
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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)

J.-F. BERNARDET1,*, P. SEGERS2, M. VANCANNEYT2, F. BERTHE1, K. KERSTERS2 and P. VANDAMME2

1 Unité de Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, 78352 Jouy-en-Josas Cedex, France
2 Laboratorium voor Microbiologie, Faculteit Wetenschappen, University of Ghent, B-9000 Ghent, Belgium

* Corresponding author. Phone: (33) 1 34-65-25-87. Fax: (33) 1 34-65-25-91.

ABSTRACT

The phylogenetic positions and G+C contents of most species belonging to the genera Flavobacterium, Cytophaga, and Flexibacter and several related taxa were determined. Most of the strains included in this study belong to rRNA superfamily V, as shown by DNA-rRNA hybridization data, but the three main genera are highly polyphyletic. Several so-called Cytophaga and Flexibacter species isolated from soil and freshwater cluster with the type species of the genus Flavobacterium, Flavobacterium aquatile, and with Flavobacterium branchiophilum. The fatty acid and protein profiles of members of this group of organisms were determined. We provide an emended description of the genus Flavobacterium and propose new combinations for the following 7 of the 10 validly described species included in this genus: Flavobacterium columnare, Flavobacterium flevense, Flavobacterium johnsoniae (we also correct the specific epithet of this taxon), Flavobacterium pectinovarum, Flavobacterium psychrophilum, Flavobacterium saccharophilum, and Flavobacterium succinicans. A new name, Flavobacterium hydatis, is proposed for [Cytophaga] aquatilis Strohl and Tait 1978. The emended genus Flavobacterium contains bacteria that have the following main characteristics: gram-negative rods that are motile by gliding, produce yellow colonies on agar, are chemoorganotrophs and aerobes, decompose several polysaccharides but not cellulose, and are widely distributed in soil and freshwater habitats. Three Flavobacterium species are pathogenic for fish. The G+C contents of Flavobacterium DNAs range from 32 to 37 mol%. An emended description of the family Flavobacteriaceae is also provided.




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Int. J. Syst. Evol. Microbiol.Home page
S. C. K. Lau, M. M. Y. Tsoi, X. Li, I. Plakhotnikova, S. Dobretsov, P.-K. Wong, J. R. Pawlik, and P.-Y. Qian
Nonlabens tegetincola gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a microbial mat in a subtropical estuary
Int J Syst Evol Microbiol, November 1, 2005; 55(6): 2279 - 2283.
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Int. J. Syst. Evol. Microbiol.Home page
S. C. K. Lau, M. M. Y. Tsoi, X. Li, I. Plakhotnikova, S. Dobretsov, P.-K. Wong, and P.-Y. Qian
Gramella portivictoriae sp. nov., a novel member of the family Flavobacteriaceae isolated from marine sediment
Int J Syst Evol Microbiol, November 1, 2005; 55(6): 2497 - 2500.
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Int. J. Syst. Evol. Microbiol.Home page
O. I. Nedashkovskaya, S. B. Kim, A. M. Lysenko, M. S. Park, V. V. Mikhailov, K. S. Bae, and H. Y. Park
Roseivirga echinicomitans sp. nov., a novel marine bacterium isolated from the sea urchin Strongylocentrotus intermedius, and emended description of the genus Roseivirga
Int J Syst Evol Microbiol, September 1, 2005; 55(5): 1797 - 1800.
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Int. J. Syst. Evol. Microbiol.Home page
S.-Y. Jung, S.-J. Kang, M.-H. Lee, S.-Y. Lee, T.-K. Oh, and J.-H. Yoon
Gaetbulibacter saemankumensis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat sediment in Korea
Int J Syst Evol Microbiol, September 1, 2005; 55(5): 1845 - 1849.
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Int. J. Syst. Evol. Microbiol.Home page
H. de Beer, C. J. Hugo, P. J. Jooste, A. Willems, M. Vancanneyt, T. Coenye, and P. A. R. Vandamme
Chryseobacterium vrystaatense sp. nov., isolated from raw chicken in a chicken-processing plant
Int J Syst Evol Microbiol, September 1, 2005; 55(5): 2149 - 2153.
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Int. J. Syst. Evol. Microbiol.Home page
L. A. O'Sullivan, J. Rinna, G. Humphreys, A. J. Weightman, and J. C. Fry
Fluviicola taffensis gen. nov., sp. nov., a novel freshwater bacterium of the family Cryomorphaceae in the phylum 'Bacteroidetes'
Int J Syst Evol Microbiol, September 1, 2005; 55(5): 2189 - 2194.
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Int. J. Syst. Evol. Microbiol.Home page
J. P. Bowman and D. S. Nichols
Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including Subsaximicrobium wynnwilliamsii gen. nov., sp. nov., Subsaximicrobium saxinquilinus sp. nov., Subsaxibacter broadyi gen. nov., sp. nov., Lacinutrix copepodicola gen. nov., sp. nov., and novel species of the genera Bizionia, Gelidibacter and Gillisia
Int J Syst Evol Microbiol, July 1, 2005; 55(4): 1471 - 1486.
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Infect. Immun.Home page
M. Soule, K. Cain, S. LaFrentz, and D. R. Call
Combining Suppression Subtractive Hybridization and Microarrays To Map the Intraspecies Phylogeny of Flavobacterium psychrophilum
Infect. Immun., June 1, 2005; 73(6): 3799 - 3802.
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Int. J. Syst. Evol. Microbiol.Home page
M. A. Horn, J. Ihssen, C. Matthies, A. Schramm, G. Acker, and H. L. Drake
Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov., Paenibacillus anaericanus sp. nov. and Paenibacillus terrae strain MH72, N2O-producing bacteria isolated from the gut of the earthworm Aporrectodea caliginosa
Int J Syst Evol Microbiol, May 1, 2005; 55(3): 1255 - 1265.
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Int. J. Syst. Evol. Microbiol.Home page
K. K. Kim, M. K. Kim, J. H. Lim, H. Y. Park, and S.-T. Lee
Transfer of Chryseobacterium meningosepticum and Chryseobacterium miricola to Elizabethkingia gen. nov. as Elizabethkingia meningoseptica comb. nov. and Elizabethkingia miricola comb. nov.
Int J Syst Evol Microbiol, May 1, 2005; 55(3): 1287 - 1293.
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Int. J. Syst. Evol. Microbiol.Home page
H. Yi, H.-M. Oh, J.-H. Lee, S.-J. Kim, and J. Chun
Flavobacterium antarcticum sp. nov., a novel psychrotolerant bacterium isolated from the Antarctic
Int J Syst Evol Microbiol, March 1, 2005; 55(2): 637 - 641.
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Int. J. Syst. Evol. Microbiol.Home page
Z. Aslam, W.-T. Im, M. K. Kim, and S.-T. Lee
Flavobacterium granuli sp. nov., isolated from granules used in a wastewater treatment plant
Int J Syst Evol Microbiol, March 1, 2005; 55(2): 747 - 751.
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Int. J. Syst. Evol. Microbiol.Home page
S. Van Trappen, I. Vandecandelaere, J. Mergaert, and J. Swings
Flavobacterium fryxellicola sp. nov. and Flavobacterium psychrolimnae sp. nov., novel psychrophilic bacteria isolated from microbial mats in Antarctic lakes
Int J Syst Evol Microbiol, March 1, 2005; 55(2): 769 - 772.
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Int. J. Syst. Evol. Microbiol.Home page
J.-H. Yoon, S.-J. Kang, and T.-K. Oh
Tenacibaculum lutimaris sp. nov., isolated from a tidal flat in the Yellow Sea, Korea
Int J Syst Evol Microbiol, March 1, 2005; 55(2): 793 - 798.
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Int. J. Syst. Evol. Microbiol.Home page
J.-H. Yoon, S.-J. Kang, C.-H. Lee, and T.-K. Oh
Marinicola seohaensis gen. nov., sp. nov., isolated from sea water of the Yellow Sea, Korea
Int J Syst Evol Microbiol, March 1, 2005; 55(2): 859 - 863.
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Int. J. Syst. Evol. Microbiol.Home page
O. I. Nedashkovskaya, S. B. Kim, K. H. Lee, K. S. Bae, G. M. Frolova, V. V. Mikhailov, and I. S. Kim
Pibocella ponti gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi
Int J Syst Evol Microbiol, January 1, 2005; 55(1): 177 - 181.
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Int. J. Syst. Evol. Microbiol.Home page
O. I. Nedashkovskaya, S. B. Kim, A. M. Lysenko, G. M. Frolova, V. V. Mikhailov, K. H. Lee, and K. S. Bae
Description of Aquimarina muelleri gen. nov., sp. nov., and proposal of the reclassification of [Cytophaga] latercula Lewin 1969 as Stanierella latercula gen. nov., comb. nov.
Int J Syst Evol Microbiol, January 1, 2005; 55(1): 225 - 229.
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Int. J. Syst. Evol. Microbiol.Home page
O. I. Nedashkovskaya, S. B. Kim, D. H. Lee, A. M. Lysenko, L. S. Shevchenko, G. M. Frolova, V. V. Mikhailov, K. H. Lee, and K. S. Bae
Roseivirga ehrenbergii gen. nov., sp. nov., a novel marine bacterium of the phylum 'Bacteroidetes', isolated from the green alga Ulva fenestrata
Int J Syst Evol Microbiol, January 1, 2005; 55(1): 231 - 234.
[Abstract] [Full Text] [PDF]


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Int. J. Syst. Evol. Microbiol.Home page
M. K. Kim, W.-T. Im, Y. K. Shin, J. H. Lim, S.-H. Kim, B. C. Lee, M.-Y. Park, K. Y. Lee, and S.-T. Lee
Kaistella koreensis gen. nov., sp. nov., a novel member of the Chryseobacterium-Bergeyella-Riemerella branch
Int J Syst Evol Microbiol, November 1, 2004; 54(6): 2319 - 2324.
[Abstract] [Full Text] [PDF]


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Int. J. Syst. Evol. Microbiol.Home page
O. I. Nedashkovskaya, S. B. Kim, S. K. Han, M.-S. Rhee, A. M. Lysenko, M. Rohde, N. V. Zhukova, G. M. Frolova, V. V. Mikhailov, and K. S. Bae
Algibacter lectus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from green algae
Int J Syst Evol Microbiol, July 1, 2004; 54(4): 1257 - 1261.
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Int. J. Syst. Evol. Microbiol.Home page
J. H. Sohn, J.-H. Lee, H. Yi, J. Chun, K. S. Bae, T.-Y. Ahn, and S.-J. Kim
Kordia algicida gen. nov., sp. nov., an algicidal bacterium isolated from red tide
Int J Syst Evol Microbiol, May 1, 2004; 54(3): 675 - 680.
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Int. J. Syst. Evol. Microbiol.Home page
E. P. Ivanova, Y. V. Alexeeva, S. Flavier, J. P. Wright, N. V. Zhukova, N. M. Gorshkova, V. V. Mikhailov, D. V. Nicolau, and R. Christen
Formosa algae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae
Int J Syst Evol Microbiol, May 1, 2004; 54(3): 705 - 711.
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Int. J. Syst. Evol. Microbiol.Home page
L. Frette, N. O. G. Jorgensen, H. Irming, and N. Kroer
Tenacibaculum skagerrakense sp. nov., a marine bacterium isolated from the pelagic zone in Skagerrak, Denmark
Int J Syst Evol Microbiol, March 1, 2004; 54(2): 519 - 524.
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Int. J. Syst. Evol. Microbiol.Home page
O. I. Nedashkovskaya, M. Suzuki, A. M. Lysenko, C. Snauwaert, M. Vancanneyt, J. Swings, M. V. Vysotskii, and V. V. Mikhailov
Cellulophaga pacifica sp. nov.
Int J Syst Evol Microbiol, March 1, 2004; 54(2): 609 - 613.
[Abstract] [Full Text] [PDF]


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Int. J. Syst. Evol. Microbiol.Home page
S. Van Trappen, I. Vandecandelaere, J. Mergaert, and J. Swings
Flavobacterium degerlachei sp. nov., Flavobacterium frigoris sp. nov. and Flavobacterium micromati sp. nov., novel psychrophilic bacteria isolated from microbial mats in Antarctic lakes
Int J Syst Evol Microbiol, January 1, 2004; 54(1): 85 - 92.
[Abstract] [Full Text] [PDF]


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Int. J. Syst. Evol. Microbiol.Home page
S. Van Trappen, J. Mergaert, and J. Swings
Flavobacterium gelidilacus sp. nov., isolated from microbial mats in Antarctic lakes
Int J Syst Evol Microbiol, September 1, 2003; 53(5): 1241 - 1245.
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Int. J. Syst. Evol. Microbiol.Home page
J. P. Bowman, C. M. Nichols, and J. A. E. Gibson
Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats
Int J Syst Evol Microbiol, September 1, 2003; 53(5): 1343 - 1355.
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Int. J. Syst. Evol. Microbiol.Home page
C. J. Hugo, P. Segers, B. Hoste, M. Vancanneyt, and K. Kersters
Chryseobacterium joostei sp. nov., isolated from the dairy environment
Int J Syst Evol Microbiol, May 1, 2003; 53(3): 771 - 777.
[Abstract] [Full Text] [PDF]


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Int. J. Syst. Evol. Microbiol.Home page
F. Zhu, S. Wang, and P. Zhou
Flavobacterium xinjiangense sp. nov. and Flavobacterium omnivorum sp. nov., novel psychrophiles from the China No. 1 glacier
Int J Syst Evol Microbiol, May 1, 2003; 53(3): 853 - 857.
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Int. J. Syst. Evol. Microbiol.Home page
H. Tamaki, S. Hanada, Y. Kamagata, K. Nakamura, N. Nomura, K. Nakano, and M. Matsumura
Flavobacterium limicola sp. nov., a psychrophilic, organic-polymer-degrading bacterium isolated from freshwater sediments
Int J Syst Evol Microbiol, March 1, 2003; 53(2): 519 - 526.
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J Antimicrob ChemotherHome page
T. Naas, S. Bellais, and P. Nordmann
Molecular and biochemical characterization of a carbapenem-hydrolysing {beta}-lactamase from Flavobacterium johnsoniae
J. Antimicrob. Chemother., February 1, 2003; 51(2): 267 - 273.
[Abstract] [Full Text] [PDF]


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Int. J. Syst. Evol. Microbiol.Home page
O. I. Nedashkovskaya, M. Suzuki, M. V. Vysotskii, and V. V. Mikhailov
Reichenbachia agariperforans gen. nov., sp. nov., a novel marine bacterium in the phylum Cytophaga-Flavobacterium-Bacteroides
Int J Syst Evol Microbiol, January 1, 2003; 53(1): 81 - 85.
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Int. J. Syst. Evol. Microbiol.Home page
P. Kampfer, U. Dreyer, A. Neef, W. Dott, and H.-J. Busse
Chryseobacterium defluvii sp. nov., isolated from wastewater
Int J Syst Evol Microbiol, January 1, 2003; 53(1): 93 - 97.
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Antimicrob. Agents Chemother.Home page
H. Mammeri, S. Bellais, and P. Nordmann
Chromosome-Encoded {beta}-Lactamases TUS-1 and MUS-1 from Myroides odoratus and Myroides odoratimimus (Formerly Flavobacterium odoratum), New Members of the Lineage of Molecular Subclass B1 Metalloenzymes
Antimicrob. Agents Chemother., November 1, 2002; 46(11): 3561 - 3567.
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Antimicrob. Agents Chemother.Home page
S. Bellais, D. Girlich, A. Karim, and P. Nordmann
EBR-1, a Novel Ambler Subclass B1 {beta}-Lactamase from Empedobacter brevis
Antimicrob. Agents Chemother., October 1, 2002; 46(10): 3223 - 3227.
[Abstract] [Full Text] [PDF]


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J. Bacteriol.Home page
D. W. Hunnicutt, M. J. Kempf, and M. J. McBride
Mutations in Flavobacterium johnsoniae gldF and gldG Disrupt Gliding Motility and Interfere with Membrane Localization of GldA
J. Bacteriol., May 1, 2002; 184(9): 2370 - 2378.
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MicrobiologyHome page
F. Berlutti, C. Passariello, L. Selan, M. C. Thaller, and G. M. Rossolini
The Chryseobacterium meningosepticum PafA enzyme: prototype of a new enzyme family of prokaryotic phosphate-irrepressible alkaline phosphatases?
Microbiology, October 1, 2001; 147(10): 2831 - 2839.
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J. Bacteriol.Home page
D. W. Hunnicutt and M. J. McBride
Cloning and Characterization of the Flavobacterium johnsoniae Gliding Motility Genes gldD and gldE
J. Bacteriol., July 15, 2001; 183(14): 4167 - 4175.
[Abstract] [Full Text] [PDF]


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Appl. Environ. Microbiol.Home page
S. Nikoskelainen, S. Salminen, G. Bylund, and A. C. Ouwehand
Characterization of the Properties of Human- and Dairy-Derived Probiotics for Prevention of Infectious Diseases in Fish
Appl. Envir. Microbiol., June 1, 2001; 67(6): 2430 - 2435.
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Appl. Environ. Microbiol.Home page
P. Secades, B. Alvarez, and J. A. Guijarro
Purification and Characterization of a Psychrophilic, Calcium-Induced, Growth-Phase-Dependent Metalloprotease from the Fish Pathogen Flavobacterium psychrophilum
Appl. Envir. Microbiol., June 1, 2001; 67(6): 2436 - 2444.
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Appl. Environ. Microbiol.Home page
E. M. Crump, M. B. Perry, S. C. Clouthier, and W. W. Kay
Antigenic Characterization of the Fish Pathogen Flavobacterium psychrophilum
Appl. Envir. Microbiol., February 1, 2001; 67(2): 750 - 759.
[Abstract] [Full Text]


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Appl. Environ. Microbiol.Home page
E. Barbieri, L. Potenza, I. Rossi, D. Sisti, G. Giomaro, S. Rossetti, C. Beimfohr, and V. Stocchi
Phylogenetic Characterization and In Situ Detection of a Cytophaga-Flexibacter-Bacteroides Phylogroup Bacterium in Tuber borchii Vittad. Ectomycorrhizal Mycelium
Appl. Envir. Microbiol., November 1, 2000; 66(11): 5035 - 5042.
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Appl. Environ. Microbiol.Home page
A. Teske, T. Brinkhoff, G. Muyzer, D. P. Moser, J. Rethmeier, and H. W. Jannasch
Diversity of Thiosulfate-Oxidizing Bacteria from Marine Sediments and Hydrothermal Vents
Appl. Envir. Microbiol., August 1, 2000; 66(8): 3125 - 3133.
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Appl. Environ. Microbiol.Home page
S. C. Park, I. Shimamura, M. Fukunaga, K.-I. Mori, and T. Nakai
Isolation of Bacteriophages Specific to a Fish Pathogen, Pseudomonas plecoglossicida, as a Candidate for Disease Control
Appl. Envir. Microbiol., April 1, 2000; 66(4): 1416 - 1422.
[Abstract] [Full Text]




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