Name: Flavobacterium frigoris R-9014
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5537

Type strain:

Species: Flavobacterium frigoris

Strain Designation: R-9014

Culture col. no.: DSM 15719, CIP 108385, LMG 21922

Strain history: CIP <- 2004, DSMZ <- S. Van Trappen, Univ. Ghent, Belgium: strain R-9014

NCBI tax ID(s): 229204 (species)

SI-ID 127366

LMG 21922, DSM 15719, CIP 108385, NBRC 102678

Special Collections

Section

When using BacDive for research please cite our paper

Flavobacterium frigoris R-9014 is a psychrophilic, Gram-negative, rod-shaped bacterium that was isolated from microbial mat.

Gram-negative
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 frigoris**
	Full Scientific Name (LPSN)	Flavobacterium frigoris Van Trappen et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #30030]	Gram stain	negative
[Ref.: #119466]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.5
[Ref.: #125438]	Gram stain	negative Confidence in %99

[Ref.: #30030]	Cell length	03-04 µm

[Ref.: #30030]	Cell shape	rod-shaped
[Ref.: #119466]	Cell shape	rod-shaped

[Ref.: #119466]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %95

[Ref.: #30030]	Pigment production	yes
[Ref.: #119466]	Pigment production	no
[Ref.: #119466]	Pigment name	Flexirubin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6077]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #6077]

Culture medium growth

[Ref.: #6077]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6077]

Culture medium composition

expand / minimize

[Ref.: #39693]

Culture medium

MEDIUM 372 - for Aquabacterium

[Ref.: #39693]

Culture medium growth

[Ref.: #39693]

Culture medium composition

expand / minimize

[Ref.: #119466]

Culture medium

CIP Medium 372

[Ref.: #119466]

Culture medium growth

[Ref.: #119466]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6077]		growth	20 °C
[Ref.: #30030]		growth	05-25 °C
[Ref.: #30030]		optimum	15 °C
[Ref.: #39693]		growth	20 °C
[Ref.: #119466]		growth	5-25 °C
[Ref.: #119466]	negative	growth	30 °C
[Ref.: #119466]	negative	growth	37 °C
[Ref.: #119466]	negative	growth	41 °C
[Ref.: #119466]	negative	growth	45 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %94.1

[Ref.: #125439]	Ability of spore formation	no Confidence in %99.2
[Ref.: #125438]	Ability of spore formation	no Confidence in %91.785

	Salt	Tested relation		Salt conc.
[Ref.: #30030]	NaCl		growth	0-2	%
[Ref.: #30030]	NaCl		optimum	1	%
[Ref.: #119466]	NaCl		growth	0-4	%
[Ref.: #119466]	NaCl	no	growth	6	%
[Ref.: #119466]	NaCl	no	growth	8	%
[Ref.: #119466]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #119466]	citrate ChEBI	-	carbon source
[Ref.: #30030]	esculin ChEBI	+	hydrolysis
[Ref.: #119466]	esculin ChEBI	-	hydrolysis
[Ref.: #119466]	hippurate ChEBI	-	hydrolysis
[Ref.: #119466]	nitrate ChEBI	-	reduction
[Ref.: #119466]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #119466]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #119466]		acetoin ChEBI	-
[Ref.: #119466]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #119466]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #119466]	amylase	+
[Ref.: #119466]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #119466]	caseinase	+	3.4.21.50
[Ref.: #30030]	catalase	+	1.11.1.6
[Ref.: #119466]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #30030]	cytochrome oxidase	+	1.9.3.1
[Ref.: #119466]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #119466]	gelatinase	-
[Ref.: #119466]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #119466]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #119466]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #119466]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #119466]	oxidase	-
[Ref.: #119466]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #119466]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #119466]	tryptophan deaminase	-
[Ref.: #119466]	tween esterase	-
[Ref.: #119466]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #119466]	11138	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	-	+	-	-

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

[Ref.: #6077]	Sample type/isolated from	microbial mat
[Ref.: #6077]	Geographic location (country and/or sea, region)	Vestfold Hills, Watts Lake
[Ref.: #6077]	Continent	Australia and Oceania

[Ref.: #119466]	Sample type/isolated from	Microbial material
[Ref.: #119466]	Country	Antarctica
[Ref.: #119466]	Country ISO 3 Code	ATA
[Ref.: #119466]	Continent	Antarctica
* marker position based on {}

Isolation sources categories

#Environmental

#Microbial community

#Microbial mat

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ557887 (>99% sequence identity) for Flavobacterium from Microbeatlas

Aquatic Samples	920
Soil Samples	118
Animal Samples	102
Plant Samples	225
Total Samples	1365

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

[Ref.: #6077]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119466]	Biosafety level	1	Risk group (French classification)

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

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #6077]	Flavobacterium frigoris 16S rRNA gene, strain LMG 21922	AJ557887	1468	GenBank ENA	229204 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Flavobacterium frigoris DSM 15719	GCA_900111075	scaffold	GenBank ENA	229204 tax ID	*
[Ref.: #66792]	Flavobacterium frigoris strain DSM 15719	229204.10	wgs	PATRIC	229204 tax ID	*
[Ref.: #66792]	Flavobacterium frigoris DSM 15719	2693429909	draft	JGI IMG/M	229204 tax ID	*

[Ref.: #30030]

GC-content

33.1-34.4 mol%

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 frigoris DSM 15719 NCBI: GCA_900111075.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	99	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	93.024	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	84.326	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	91.785	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98.177	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 frigoris DSM 15719 NCBI: GCA_900111075
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.2
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	64.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	94.1

Availability in culture collections External links

[Ref.: #6077]

Culture collection no.

DSM 15719, CIP 108385, LMG 21922

[Ref.: #75020]

SI-ID 127366

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavobacterium turcicum sp. nov. and Flavobacterium kayseriense sp. nov. isolated from farmed rainbow trout in Turkey.	Saticioglu IB, Ay H, Altun S, Duman M, Sahin N	Syst Appl Microbiol	10.1016/j.syapm.2021.126186	2021	*
Phylogeny	Flavobacterium beibuense sp. nov., isolated from marine sediment.	Fu Y, Tang X, Lai Q, Zhang C, Zhong H, Li W, Liu Y, Chen L, Sun F, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.018846-0	2010	*
Phylogeny	Flavobacterium degerlachei sp. nov., Flavobacterium frigoris sp. nov. and Flavobacterium micromati sp. nov., novel psychrophilic bacteria isolated from microbial mats in Antarctic lakes.	Van Trappen S, Vandecandelaere I, Mergaert J, Swings J	Int J Syst Evol Microbiol	10.1099/ijs.0.02857-0	2004	*

References

#6077

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15719

#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 )

#30030

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26394 (see below)

#39693 ; 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 .

#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 .

#75020

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-ID127366.1 )

#119466 Collection of Institut Pasteur ; Curators of the CIP; CIP 108385

#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 .

#26394

IJSEM 85 2004 ( DOI 10.1099/ijs.0.02857-0 , PubMed 14742463 )

* These data were automatically processed and therefore are not curated

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Flavobacterium frigoris DSM 15719

Flavobacterium frigoris DSM 15719

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