Flavobacterium frigidimaris (DSM 15937, CCUG 59364, JCM 12218)

Name: Flavobacterium frigidimaris (DSM 15937, CCUG 59364, JCM 12218)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5538

Type strain

Strain Designation KUC-1

Culture col. no. DSM 15937 CCUG 59364 JCM 12218 CIP 109029 KUC-1

NCBI tax ID(s) 262320

Special Collections DSMZ CCUG JCM CIP

Links

Flavobacterium frigidimaris KUC-1 is an aerobe, psychrophilic, Gram-negative prokaryote that was isolated from sea water.

Gram-negative rod-shaped aerobe psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 265601

JCM 12218,DSM 15937,CIP 109029,CCUG 59364

@ref 20215

Last LPSN update 2025-12-16 09:48:05

Domain Pseudomonadati

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Flavobacterium

Species Flavobacterium frigidimaris

Full scientific name Flavobacterium frigidimaris Nogi et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
119464	negative	rod-shaped
125438			90.5
125438	negative		99.227
125439	negative		99.9

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6196	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
119464	CIP Medium 72	Medium recipe at CIP
119464	CIP Medium 328	Medium recipe at CIP
119464	CIP Medium 566	Medium recipe at CIP
6196	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6196	positive	growth	20	psychrophilic
61941	positive	growth	20-30
67770	positive	growth	20	psychrophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
61941	aerobe
119464	obligate aerobe
125439	obligate aerobe	96.5

Spore formation

@ref	Spore formation	Confidence
125439		99

Observation

67770

Observationquinones: MK-6

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	+	3.2.1.31	from API zym
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
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68382	trypsin	-	3.4.21.4	from API zym
68382	valine arylamidase	+		from API zym

Fatty acid profile

Metadata FA analysis

@ref

61941

Fatty acid	Percentage	ECL
C15:0 ISO	28.2	14.621
C16:1 ω7c	19.2	15.819
C15:0 ISO 3OH	7.7	16.135
C17:0 iso 3OH	5.9	18.161
C15:0	5.5	15
C17:1 ω9c ISO	4.3	16.416
C15:1 ω6c	4.1	14.856
C15:1 ISO G	3.7	14.441
C16:0 3OH	3.5	17.52
C17:1 ω6c	3.5	16.862
C15:0 ANTEISO	3.2	14.711
C16:0	2.3	16
C17:1 ISO I/C16:0 DMA	2	16.481
C16:0 iso 3OH	1.6	17.145
unknown 13.566	1.3	13.566
C14:0	1.1	14
C16:1 ISO H	1	15.461
C16:0 iso	1	15.626
unknown 11.541	0.8	11.541

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
119464	-	+	+	+	-	+	+	-	-	-	+	+	+	+	+	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Sampling date	Country	Country ISO 3 Code	Continent
6196	sea water				Australia and Oceania
61941	Seawater	2003	Antarctica	ATA	Australia and Oceania
67770	Antarctic seawater
119464	Environment, Seawater		Antarctica	ATA	Antarctica

Taxonmaps

69479

Global distribution of 16S sequence JX657051 (>99% sequence identity) for Flavobacterium from Microbeatlas

Aquatic Samples	282
Soil Samples	399
Animal Samples	390
Plant Samples	88
Total Samples	1159

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6196	1	Risk group (German classification) According to TRBA 466
119464	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
67770	ASM221727v1 assembly for Flavobacterium frigidimaris DSM 15937	scaffold	GCA_002217275	262320.7	8114414589	262320	64.3
67770	IMG-taxon 2695420960 annotated assembly for Flavobacterium frigidimaris DSM 15937	scaffold	GCA_900129595	262320.5	2695420960	262320	44

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Flavobacterium frigidimaris gene for 16S ribosomal RNA, partial sequence	AB183888	1424		262320
20218	Flavobacterium frigidimaris strain KUC-1 16S ribosomal RNA gene, partial sequence	JX657051	1222		262320

GC content

@ref	GC-content (mol%)	Method
67770	34.5	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Flavobacterium frigidimaris DSM 15937
NCBI: GCA_900129595

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.00	no
125439	motility	BacteriaNetⓘ	no	63.60	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Flavobacterium frigidimaris strain DSM 15937
PATRIC: 262320.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.23	no
125438	anaerobic	anaerobicⓘ	no	98.70	yes
125438	spore-forming	spore-formingⓘ	no	89.47	no
125438	aerobic	aerobicⓘ	yes	89.19	no
125438	thermophilic	thermophileⓘ	no	98.84	yes
125438	flagellated	motile2+ⓘ	no	90.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Crystal structure of binary and ternary complexes of archaeal UDP-galactose 4-epimerase-like L-threonine dehydrogenase from Thermoplasma volcanium.	Yoneda K, Sakuraba H, Araki T, Ohshima T	J Biol Chem	10.1074/jbc.M111.336958	2012
Enzymology	Crystal structure of UDP-galactose 4-epimerase-like L-threonine dehydrogenase belonging to the intermediate short-chain dehydrogenase-reductase superfamily.	Yoneda K, Sakuraba H, Muraoka I, Oikawa T, Ohshima T	FEBS J	10.1111/j.1742-4658.2010.07916.x	2010
Enzymology	Crystallization and preliminary X-ray diffraction studies of tetrameric malate dehydrogenase from the novel Antarctic psychrophile Flavobacterium frigidimaris KUC-1.	Fujii T, Oikawa T, Muraoka I, Soda K, Hata Y	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/S1744309107051524	2007
Enzymology	A cold-active and thermostable alcohol dehydrogenase of a psychrotorelant from Antarctic seawater, Flavobacterium frigidimaris KUC-1.	Kazuoka T, Oikawa T, Muraoka I, Kuroda S, Soda K	Extremophiles	10.1007/s00792-006-0034-1	2006
Enzymology	Purification, characterization, and overexpression of psychrophilic and thermolabile malate dehydrogenase of a novel antarctic psychrotolerant, Flavobacterium frigidimaris KUC-1.	Oikawa T, Yamamoto N, Shimoke K, Uesato S, Ikeuchi T, Fujioka T	Biosci Biotechnol Biochem	10.1271/bbb.69.2146	2005
Phylogeny	Flavobacterium tructae sp. nov. and Flavobacterium piscis sp. nov., isolated from farmed rainbow trout (Oncorhynchus mykiss).	Zamora L, Vela AI, Sanchez-Porro C, Palacios MA, Moore ERB, Dominguez L, Ventosa A, Fernandez-Garayzabal JF	Int J Syst Evol Microbiol	10.1099/ijs.0.056341-0	2013
Phylogeny	Flavobacterium aquidurense sp. nov. and Flavobacterium hercynium sp. nov., from a hard-water creek.	Cousin S, Pauker O, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.64556-0	2007
Phylogeny	Flavobacterium frigidimaris sp. nov., isolated from Antarctic seawater.	Nogi Y, Soda K, Oikawa T	Syst Appl Microbiol	10.1016/j.syapm.2005.01.001	2005

References

#6196	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15937
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#61941	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 59364
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#119464	Collection of Institut Pasteur ; Curators of the CIP; CIP 109029
#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 .
#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 frigidimaris (DSM 15937, CCUG 59364, JCM 12218)

Name and taxonomic classification