Name: Flavobacterium columnare CIP 103533
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 139541

Type strain:

Species: Flavobacterium columnare

Culture col. no.: CIP 103533, ATCC 49512

Strain history: CIP <- 1993, ATCC <- 1992, J.F. Bernardet, INRA, Jouy en Josas, France: strain TG 44/87, Flexibacter columnaris

NCBI tax ID(s): 1041826 (strain), 996 (species)

SI-ID 42527

ATCC 49512, CIP 103533

Special Collections

Other strains from Flavobacterium columnare

Section

When using BacDive for research please cite our paper

Flavobacterium columnare CIP 103533 is a psychrophilic, Gram-negative, motile bacterium of the family Flavobacteriaceae.

Gram-negative
motile
rod-shaped
psychrophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Flavobacterium*
	Species	**Flavobacterium columnare**
	Full Scientific Name (LPSN)	Flavobacterium columnare (Bernardet and Grimont 1989 ex Davis 1922) Bernardet et al. 1996

	Synonym	Cytophaga columnaris
	Synonym	Flexibacter columnaris

Information on morphological and physiological properties Morphology

[Ref.: #41892]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %97.085
[Ref.: #125439]	Gram stain	negative Confidence in %99.6

[Ref.: #41892]	Cell shape	rod-shaped

[Ref.: #41892]	Motility	yes
[Ref.: #125438]	Motility	no Confidence in %95

Information on culture and growth conditions Culture and growth conditions

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Culture medium

MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

CIP Medium 566

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium

CIP Medium 3

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #41892]		growth	22 °C
[Ref.: #41892]		growth	10-37 °C
[Ref.: #41892]	negative	growth	5 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125438]	Ability of spore formation	no Confidence in %90.709
[Ref.: #125439]	Ability of spore formation	no Confidence in %98.2

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #41892]	nitrate ChEBI	-	reduction
[Ref.: #41892]	nitrite ChEBI	-	reduction
[Ref.: #41892]	sodium thiosulfate ChEBI	-	builds gas from

	Metabolite production	Metabolite	Production
[Ref.: #41892]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #41892]	beta-galactosidase	-	3.2.1.23
[Ref.: #41892]	caseinase	-	3.4.21.50
[Ref.: #41892]	catalase	+	1.11.1.6
[Ref.: #41892]	gelatinase	+
[Ref.: #41892]	lipase	-
[Ref.: #41892]	oxidase	+
[Ref.: #41892]	urease	-	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	purine metabolism	68.09	64 of 94
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	molybdenum cofactor biosynthesis	55.56	5 of 9
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	alanine metabolism	55.17	16 of 29
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	53.57	15 of 28
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	histidine metabolism	41.38	12 of 29
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	oxidative phosphorylation	37.36	34 of 91
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	valine metabolism	33.33	3 of 9
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	25	3 of 12
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #41892]	Sample type/isolated from	Animal, Brown trout fry, skin lesions
[Ref.: #41892]	Geographic location (country and/or sea, region)	Villedieu les Poêles
[Ref.: #41892]	Country	France
[Ref.: #41892]	Country ISO 3 Code	FRA
[Ref.: #41892]	Continent	Europe
[Ref.: #41892]	Isolation date	1987

[Ref.: #41892]	Geographic location (country and/or sea, region)	Villedieu-les-Poeles
[Ref.: #41892]	Country	France
[Ref.: #41892]	Country ISO 3 Code	FRA
[Ref.: #41892]	Continent	Europe
* marker position based on {}

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #41892]

Biosafety level

Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #124043]	Flavobacterium columnare strain ATCC 49512 clone ITS-F 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence.	GU079950	684	GenBank ENA	1041826 tax ID	*
[Ref.: #124043]	Flavobacterium columnare strain ATCC 49512 clone ITS-F 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence.	GU079951	776	GenBank ENA	1041826 tax ID	*
[Ref.: #124043]	Flavobacterium columnare strain ATCC 49512 clone ITS-F 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence.	GU079952	786	GenBank ENA	1041826 tax ID	*
[Ref.: #124043]	Flavobacterium columnare strain ATCC 49512 clone ITS-F 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence.	GU079953	785	GenBank ENA	1041826 tax ID	*
[Ref.: #124043]	Flavobacterium columnare strain ATCC 49512 clone ITS-F 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence.	GU079954	787	GenBank ENA	1041826 tax ID	*
[Ref.: #124043]	Flavobacterium columnare strain ATCC 49512 clone ITS-F 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence.	GU079955	847	GenBank ENA	1041826 tax ID	*
[Ref.: #124043]	Flavobacterium columnare strain ATCC 49512 16S ribosomal RNA gene, partial sequence.	AY635167	1459	GenBank ENA	1041826 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Flavobacterium columnare ATCC 49512	GCA_000240075	complete	GenBank ENA	1041826 tax ID	*
[Ref.: #66792]	Flavobacterium columnare ATCC 49512	1041826.3	complete	PATRIC	1041826 tax ID	*
[Ref.: #66792]	Flavobacterium columnare ATCC 49512	2511231122	complete	JGI IMG/M	1041826 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Flavobacterium columnare ATCC 49512 ATCC 49512 NCBI: GCA_000240075.2
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	97.085	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.651	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	82.952	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	90.709	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95.623	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	95	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Flavobacterium columnare ATCC 49512 NCBI: GCA_000240075
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	84.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	50.3
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.2

Availability in culture collections External links

[Ref.: #41892]

Culture collection no.

CIP 103533, ATCC 49512

[Ref.: #96023]

SI-ID 42527

Literature:

	Title	Authors	Journal	DOI	Year
Genetics	Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512.	Tekedar HC, Karsi A, Reddy JS, Nho SW, Kalindamar S, Lawrence ML	Front Microbiol	10.3389/fmicb.2017.00588	2017	*
Genetics	Genome sequence of the fish pathogen Flavobacterium columnare ATCC 49512.	Tekedar HC, Karsi A, Gillaspy AF, Dyer DW, Benton NR, Zaitshik J, Vamenta S, Banes MM, Gulsoy N, Aboko-Cole M, Waldbieser GC, Lawrence ML	J Bacteriol	10.1128/JB.00281-12	2012	*
Pathogenicity	Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen.	Laanto E, Ravantti JJ, Sundberg LR	Microorganisms	10.3390/microorganisms8121919	2020	*
	Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes.	Kumru S, Tekedar HC, Gulsoy N, Waldbieser GC, Lawrence ML, Karsi A	Front Microbiol	10.3389/fmicb.2017.01375	2017	*

References

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#41892 Collection of Institut Pasteur ; Curators of the CIP; CIP 103533

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#96023

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID42527.1 )

#124043

Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

* These data were automatically processed and therefore are not curated

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Flavobacterium columnare ATCC 49512 ATCC 49512

Flavobacterium columnare ATCC 49512

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