Flavobacterium psychrophilum (DSM 21280, ATCC 49511, CIP 103535)

Name: Flavobacterium psychrophilum (DSM 21280, ATCC 49511, CIP 103535)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5530

Type strain

Strain Designation TG 02/86

Culture col. no. DSM 21280 ATCC 49511 CIP 103535 JIP 02/86 TG 02/86

NCBI tax ID(s) 96345

Special Collections DSMZ CIP

History <- J.-F. Bernardet, INRA; TG 02/86; JIP 02/86 CIP <- 1993, ATCC, Flexibacter psychrophilus <- 1992, J.F. Bernardet, INRA, Jouy en Josas, France: strain TG 02/86

Links

Flavobacterium psychrophilum TG 02/86 is a Gram-negative, rod-shaped animal pathogen that was isolated from kidney of a diseased rainbow trout fry.

Gram-negative rod-shaped animal pathogen genome sequence Bacteria

Name and taxonomic classification

SI-ID 42526

DSM 21280,ATCC 49511,CIP 103535

@ref 20215

Last LPSN update 2026-02-09 11:18:59

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Flavobacterium

Species Flavobacterium psychrophilum

Full scientific name Flavobacterium psychrophilum (Bernardet and Grimont 1989 ex Borg 1960) Bernardet et al. 1996

Synonyms (2)

Cytophaga psychrophila
Flexibacter psychrophilus

BacDive ID	Other strains from **Flavobacterium psychrophilum** (8)	Type strain
5529	F. psychrophilum 3068, DSM 3660, IAM 14308, NCMB 1947, JCM ... (type strain)
134699	F. psychrophilum CIP 109952, JIP 08/99
139028	F. psychrophilum CIP 109955, FPC 831
139581	F. psychrophilum CIP 109953, JIP 16/00
139582	F. psychrophilum LVDJ XP189, CIP 109954
139583	F. psychrophilum CIP 109956, FPC 840
139584	F. psychrophilum OSU THC02-90, CIP 109957
139585	F. psychrophilum LNPAA P01/88, CIP 103536, ATCC 49510

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
122025	negative	rod-shaped
125438			97
125438	negative		98.396

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15602	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
42074	MEDIUM 36 - for Flavobacterium psychrophilum		Distilled water make up to (1000.000 ml);Agar (10.000 g);Yeast extract (0.500 g);Sodium acetate (0.200 g);Tryptone (5.000 g);Beef extract (0.200 g)
122025	CIP Medium 566	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
15602	positive	growth	15
42074	positive	growth	22

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125438		91.203

Halophily

@ref	Salt	Growth	Tested relation	Concentration
122025	NaCl	positive	growth	0 %
122025	NaCl		growth	2 %
122025	NaCl		growth	4 %
122025	NaCl		growth	6 %
122025	NaCl		growth	8 %
122025	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
122025	16947 ChEBI	citrate	-	carbon source
122025	4853 ChEBI	esculin	-	hydrolysis
122025	606565 ChEBI	hippurate	-	hydrolysis
122025	15792 ChEBI	malonate	-	assimilation
122025	17632 ChEBI	nitrate	-	builds gas from
122025	17632 ChEBI	nitrate	-	reduction
122025	16301 ChEBI	nitrite	-	builds gas from
122025	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
122025	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122025	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
122025	15688 ChEBI	acetoin	-
122025	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
122025	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
122025	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122025	caseinase	+	3.4.21.50
122025	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
122025	gamma-glutamyltransferase	+	2.3.2.2
122025	gelatinase	-
68382	leucine arylamidase	-	3.4.11.1	from API zym
122025	lipase	+
68382	lipase (C 14)	-		from API zym
122025	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122025	ornithine decarboxylase	-	4.1.1.17
122025	oxidase	+
122025	phenylalanine ammonia-lyase	+	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
122025	tryptophan deaminase	-
122025	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122025	-	+	+	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Fishes	#Salmonidae
#Host Body-Site	#Urogenital tract	#Kidney

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
15602	kidney of a diseased rainbow trout fry	Seine Maritime	France	FRA	Europe
122025	Animal, Rainbow trout fry, kidney	Biville la Rivière	France	FRA	Europe	1986

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
15602		1	Risk group (German classification) According to TRBA 466
122025		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM6430v2 assembly for Flavobacterium psychrophilum JIP02/86	complete	GCA_000064305	402612.5	640753027	402612	99.47
124043	ASM4053877v1 assembly for Flavobacterium psychrophilum DSM 21280	contig	GCA_040538775			96345	54.06

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Flavobacterium psychrophilum JIP02/86
PATRIC: 402612.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.40	no
125438	anaerobic	anaerobicⓘ	no	97.80	no
125438	spore-forming	spore-formingⓘ	no	91.20	no
125438	aerobic	aerobicⓘ	yes	84.49	no
125438	thermophilic	thermophileⓘ	no	94.16	no
125438	flagellated	motile2+ⓘ	no	97.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Immersion challenge model for Flavobacterium psychrophilum infection of Atlantic salmon (Salmo salar L.) fry.	Macchia V, Inami M, Ramstad A, Grammes F, Reeve A, Moen T, Torgersen JS, Adams A, Desbois AP, Hoare R.	J Fish Dis	10.1111/jfd.13699	2022
Genetics	Whole-genome-based taxonomy as the most accurate approach to identify Flavobacterium species.	Gelinas V, Paquet VE, Paquet MF, Vincent AT, Charette SJ.	FEMS Microbiol Lett	10.1093/femsle/fnae089	2024
	Antibacterial Activity of Rainbow Trout Plasma: In Vitro Assays and Proteomic Analysis	Mizaeva T, Alieva K, Zulkarneev E, Kurpe S, Isakova K, Matrosova S, Borvinskaya E, Sukhovskaya I.	Animals (Basel)		2023
	Establishment of a Real-Time PCR Assay for the Detection of Devriesea agamarum in Lizards.	Brockmann M, Leineweber C, Hellebuyck T, Martel A, Pasmans F, Gentil M, Muller E, Marschang RE.	Animals (Basel)	10.3390/ani13050881	2023
	Comparative Genome Analysis Provides Insights into the Pathogenicity of Flavobacterium psychrophilum.	Castillo D, Christiansen RH, Dalsgaard I, Madsen L, Espejo R, Middelboe M.	PLoS One	10.1371/journal.pone.0152515	2016
	Complete genome sequence of the fish pathogen Flavobacterium psychrophilum ATCC 49418(T.).	Wu AK, Kropinski AM, Lumsden JS, Dixon B, MacInnes JI.	Stand Genomic Sci	10.1186/1944-3277-10-3	2015
Genetics	Bacteriophage resistance mechanisms in the fish pathogen Flavobacterium psychrophilum: linking genomic mutations to changes in bacterial virulence factors.	Castillo D, Christiansen RH, Dalsgaard I, Madsen L, Middelboe M.	Appl Environ Microbiol	10.1128/aem.03699-14	2015
Genetics	Genomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum.	Duchaud E, Rochat T, Habib C, Barbier P, Loux V, Guerin C, Dalsgaard I, Madsen L, Nilsen H, Sundell K, Wiklund T, Strepparava N, Wahli T, Caburlotto G, Manfrin A, Wiens GD, Fujiwara-Nagata E, Avendano-Herrera R, Bernardet JF, Nicolas P.	Front Microbiol	10.3389/fmicb.2018.00138	2018
	Identification of cold-temperature-regulated genes in Flavobacterium psychrophilum.	Hesami S, Metcalf DS, Lumsden JS, Macinnes JI.	Appl Environ Microbiol	10.1128/aem.01717-10	2011
	Development of genetic techniques for the psychrotrophic fish pathogen Flavobacterium psychrophilum.	Alvarez B, Secades P, McBride MJ, Guijarro JA.	Appl Environ Microbiol	10.1128/aem.70.1.581-587.2004	2004
Phylogeny	The Membrane Attack Complex/Perforin Superfamily.	Moreno-Hagelsieb G, Vitug B, Medrano-Soto A, Saier MH.	J Mol Microbiol Biotechnol	10.1159/000481286	2017
	High Genetic Diversity in Flavobacterium psychrophilum Isolates from Healthy Rainbow Trout (Oncorhynchus mykiss) Farmed in the Same Watershed, Revealed by Two Typing Methods.	Calvez S, Navarro-Gonzalez N, Siekoula-Nguedia C, Fournel C, Duchaud E.	Appl Environ Microbiol	10.1128/aem.01398-20	2021
	Two functionally distinct heme/iron transport systems are virulence determinants of the fish pathogen Flavobacterium psychrophilum.	Zhu Y, Lechardeur D, Bernardet JF, Kerouault B, Guerin C, Rigaudeau D, Nicolas P, Duchaud E, Rochat T.	Virulence	10.1080/21505594.2022.2101197	2022
	The Type IX Secretion System Is Required for Virulence of the Fish Pathogen Flavobacterium psychrophilum.	Barbier P, Rochat T, Mohammed HH, Wiens GD, Bernardet JF, Halpern D, Duchaud E, McBride MJ.	Appl Environ Microbiol	10.1128/aem.00799-20	2020
Genetics	Genomic Characterization of Flavobacterium psychrophilum Serotypes and Development of a Multiplex PCR-Based Serotyping Scheme.	Rochat T, Fujiwara-Nagata E, Calvez S, Dalsgaard I, Madsen L, Calteau A, Lunazzi A, Nicolas P, Wiklund T, Bernardet JF, Duchaud E.	Front Microbiol	10.3389/fmicb.2017.01752	2017
	Transcriptional responses of resistant and susceptible fish clones to the bacterial pathogen Flavobacterium psychrophilum.	Langevin C, Blanco M, Martin SA, Jouneau L, Bernardet JF, Houel A, Lunazzi A, Duchaud E, Michel C, Quillet E, Boudinot P.	PLoS One	10.1371/journal.pone.0039126	2012
Phylogeny	A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates.	Ashrafi R, Pulkkinen K, Sundberg LR, Pekkala N, Ketola T.	BMC Microbiol	10.1186/s12866-015-0576-4	2015
Phylogeny	Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum.	Nicolas P, Mondot S, Achaz G, Bouchenot C, Bernardet JF, Duchaud E.	Appl Environ Microbiol	10.1128/aem.00244-08	2008
Metabolism	Potential mechanisms of attenuation for rifampicin-passaged strains of Flavobacterium psychrophilum.	Gliniewicz K, Wildung M, Orfe LH, Wiens GD, Cain KD, Lahmers KK, Snekvik KR, Call DR.	BMC Microbiol	10.1186/s12866-015-0518-1	2015
	Zebrafish (Danio rerio) as an animal model for bath infection by Flavobacterium psychrophilum.	Avendano-Herrera R, Benavides I, Espina JA, Soto-Comte D, Poblete-Morales M, Valdes JA, Feijoo CG, Reyes AE	J Fish Dis	10.1111/jfd.13156	2020
Enzymology	Identification of a Novel Elastin-Degrading Enzyme from the Fish Pathogen Flavobacterium psychrophilum.	Rochat T, Perez-Pascual D, Nilsen H, Carpentier M, Bridel S, Bernardet JF, Duchaud E	Appl Environ Microbiol	10.1128/AEM.02535-18	2019
	Cytotoxic activity of Flavobacterium psychrophilum in skeletal muscle cells of rainbow trout (Oncorhynchus mykiss).	Iturriaga M, Espinoza MB, Poblete-Morales M, Feijoo CG, Reyes AE, Molina A, Avendano-Herrera R, Valdes JA	Vet Microbiol	10.1016/j.vetmic.2017.09.009	2017
Metabolism	Antigenic proteins of Flavobacterium psychrophilum recognized by ayu Plecoglossus altivelis antisera.	Kato G, Sakai T, Suzuki K, Yamaguchi K, Takano T, Matsuyama T, Nakayasu C	Dis Aquat Organ	10.3354/dao02679	2014
	Genomic structure of bacteriophage 6H and its distribution as prophage in Flavobacterium psychrophilum strains.	Castillo D, Espejo R, Middelboe M	FEMS Microbiol Lett	10.1111/1574-6968.12342	2013
Metabolism	Deoxyribonucleoside kinases in two aquatic bacteria with high specificity for thymidine and deoxyadenosine.	Tinta T, Christiansen LS, Konrad A, Liberles DA, Turk V, Munch-Petersen B, Piskur J, Clausen AR	FEMS Microbiol Lett	10.1111/j.1574-6968.2012.02565.x	2012
Genetics	Complete genome sequence of the fish pathogen Flavobacterium psychrophilum.	Duchaud E, Boussaha M, Loux V, Bernardet JF, Michel C, Kerouault B, Mondot S, Nicolas P, Bossy R, Caron C, Bessieres P, Gibrat JF, Claverol S, Dumetz F, Le Henaff M, Benmansour A	Nat Biotechnol	10.1038/nbt1313	2007
Phenotype	Different Phenotypes of Mature Biofilm in Flavobacterium psychrophilum Share a Potential for Virulence That Differs from Planktonic State.	Levipan HA, Avendano-Herrera R	Front Cell Infect Microbiol	10.3389/fcimb.2017.00076	2017

References

#15602	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21280
#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 )
#42074	; Curators of the CIP;
#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) .
#68382	Automatically annotated from API zym .
#122025	Collection of Institut Pasteur ; Curators of the CIP; CIP 103535
#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 )
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Flavobacterium psychrophilum (DSM 21280, ATCC 49511, CIP 103535)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000064305

Genome-based predictions

Predictions

Literature

Literature

References

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