Name: Flavobacterium limicola ST-82
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5535

Type strain:

Species: Flavobacterium limicola

Strain Designation: ST-82

Culture col. no.: DSM 15094, JCM 11473, CCUG 58906, LMG 21930, CIP 107957, KCTC 12494, NBRC 103156

Strain history: CIP <- 2003, JCM <- H. Tamaki: strain ST-82

NCBI tax ID(s): 180441 (species)

SI-ID 99541

LMG 21930, LMG 21949, DSM 15094, JCM 11473, CIP 107957, KCTC 12494, NBRC 103156, CCUG 58906

Special Collections

Other strains from Flavobacterium limicola

Section

When using BacDive for research please cite our paper

Flavobacterium limicola ST-82 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from river sediment.

Gram-negative
rod-shaped
aerobe
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 limicola**
	Full Scientific Name (LPSN)	Flavobacterium limicola Tamaki et al. 2003

Information on morphological and physiological properties Morphology

[Ref.: #120600]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %98.455
[Ref.: #125439]	Gram stain	negative Confidence in %99.9

[Ref.: #120600]	Cell shape	rod-shaped

[Ref.: #120600]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %91

[Ref.: #61773]

Incubation period

2-3 days

[Ref.: #120600]	Pigment production	no
[Ref.: #120600]	Pigment name	Flexirubin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5707]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #5707]

Culture medium growth

[Ref.: #5707]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5707]

Culture medium composition

expand / minimize

[Ref.: #42254]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #42254]

Culture medium growth

[Ref.: #42254]

Culture medium composition

expand / minimize

[Ref.: #120600]

Culture medium

CIP Medium 72

[Ref.: #120600]

Culture medium growth

[Ref.: #120600]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #5707]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #5707]

Culture medium growth

[Ref.: #5707]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #5707]		growth	15 °C
[Ref.: #42254]		growth	15 °C
[Ref.: #61773]		growth	20 °C
[Ref.: #67770]		growth	15 °C
[Ref.: #120600]	negative	growth	41 °C
[Ref.: #120600]	negative	growth	37 °C
[Ref.: #120600]	negative	growth	30 °C
[Ref.: #120600]	negative	growth	25 °C
[Ref.: #120600]		growth	5-15 °C
[Ref.: #120600]	negative	growth	45 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #61773]	Oxygen tolerance	aerobe
[Ref.: #120600]	Oxygen tolerance	obligate aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %99

[Ref.: #125438]	Ability of spore formation	no Confidence in %92.065
[Ref.: #125439]	Ability of spore formation	no Confidence in %98

	Salt	Tested relation		Salt conc.
[Ref.: #120600]	NaCl		growth	0	%
[Ref.: #120600]	NaCl	no	growth	2	%
[Ref.: #120600]	NaCl	no	growth	4	%
[Ref.: #120600]	NaCl	no	growth	6	%
[Ref.: #120600]	NaCl	no	growth	8	%
[Ref.: #120600]	NaCl	no	growth	10	%

[Ref.: #67770]

Observation

quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #120600]	citrate ChEBI	-	carbon source
[Ref.: #120600]	esculin ChEBI	+	hydrolysis
[Ref.: #120600]	glucose ChEBI	+	degradation
[Ref.: #120600]	hippurate ChEBI	+	hydrolysis
[Ref.: #120600]	malonate ChEBI	-	assimilation
[Ref.: #120600]	nitrate ChEBI	-	builds gas from
[Ref.: #120600]	nitrate ChEBI	-	reduction
[Ref.: #120600]	nitrite ChEBI	-	builds gas from
[Ref.: #120600]	nitrite ChEBI	-	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #120600]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	yes	no

	Metabolite production	Metabolite	Production
[Ref.: #120600]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #120600]		acetoin ChEBI	-
[Ref.: #120600]		glucose ChEBI		+

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #120600]	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.: #120600]	amylase	-
[Ref.: #120600]	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.: #120600]	caseinase	-	3.4.21.50
[Ref.: #120600]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #120600]	DNase	-
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #120600]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #120600]	gelatinase	-
[Ref.: #120600]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #120600]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #120600]	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.: #120600]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120600]	oxidase	-
[Ref.: #120600]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #120600]	protease	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #120600]	tryptophan deaminase	-
[Ref.: #120600]	tween esterase	-
[Ref.: #120600]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

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

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #120600]	2514	not determinedn.d.	+	+	-	-	-	-	-	+	-	+	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-

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.: #120600]	10775	-	+	-	-	-	+	+	-	+	-	+	+	-	-	-	+	-	+	-	-

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

[Ref.: #5707]	Sample type/isolated from	river sediment
[Ref.: #5707]	Geographic location (country and/or sea, region)	Ibaraki Pref., Shin river
[Ref.: #5707]	Country	Japan
[Ref.: #5707]	Country ISO 3 Code	JPN
[Ref.: #5707]	Continent	Asia

[Ref.: #61773]	Sample type/isolated from	Fresh water sediment
[Ref.: #61773]	Country	Japan
[Ref.: #61773]	Country ISO 3 Code	JPN
[Ref.: #61773]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Freshwater river sediments
[Ref.: #67770]	Geographic location (country and/or sea, region)	Ibaraki Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #120600]	Sample type/isolated from	Environment, Frest water sediments
[Ref.: #120600]	Country	Japan
[Ref.: #120600]	Country ISO 3 Code	JPN
[Ref.: #120600]	Continent	Asia
[Ref.: #120600]	Isolation date	1997
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#River (Creek)
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

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

[Ref.: #5707]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120600]	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.: #5707]	Flavobacterium limicola gene for 16S ribosomal RNA, strain:ST-82	AB075230	1475	GenBank ENA	180441 tax ID
[Ref.: #124043]	Flavobacterium limicola gene for 16S rRNA, partial sequence, strain: NBRC 103156.	AB455261	1439	GenBank ENA	180441 tax ID	*
[Ref.: #20218]	Flavobacterium limicola strain DSM 15094 16S ribosomal RNA gene, partial sequence	JX657041	1256	GenBank ENA	180441 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Flavobacterium limicola DSM 15094	GCA_003634755	contig	GenBank ENA	180441 tax ID	*
[Ref.: #66792]	Flavobacterium limicola strain DSM 15094	180441.4	wgs	PATRIC	180441 tax ID	*
[Ref.: #66792]	Flavobacterium limicola DSM 15094	2698536747	draft	JGI IMG/M	180441 tax ID	*

[Ref.: #5707]	GC-content	35 mol%
[Ref.: #67770]	GC-content	34 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 limicola strain DSM 15094 PATRIC: 180441.4
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.455	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	99.411	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	92.065	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	86.9	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98.174	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	91	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Flavobacterium limicola DSM 15094 NCBI: GCA_003634755
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	61.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.9
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99

Availability in culture collections External links

[Ref.: #5707]

Culture collection no.

DSM 15094, JCM 11473, CCUG 58906, LMG 21930, CIP 107957, KCTC 12494, NBRC 103156

[Ref.: #75018]

SI-ID 99541

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavobacterium laiguense sp. nov., a psychrophilic bacterium isolated from Laigu glacier on the Tibetan Plateau.	Yang LL, Liu Q, Liu HC, Zhou YG, Xin YH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003400	2019	*
Phylogeny	Flavobacterium fluvii sp. nov., isolated from stream sediment.	Lee SH, Kim JM, Lee JR, Park W, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.010850-0	2009	*
Phylogeny	Flavobacterium tiangeerense sp. nov., a cold-living bacterium isolated from a glacier.	Xin YH, Liang ZH, Zhang DC, Liu HC, Zhang JL, Yu Y, Xu MS, Zhou PJ, Zhou YG	Int J Syst Evol Microbiol	10.1099/ijs.0.007906-0	2009	*
Phylogeny	Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet.	Ali Z, Cousin S, Fruhling A, Brambilla E, Schumann P, Yang Y, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.008771-0	2009	*

References

#5707

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15094

#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 )

#42254 ; Curators of the CIP;
#61773 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 58906

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68382

Automatically annotated from API zym .

#75018

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-ID99541.1 )

#120600 Collection of Institut Pasteur ; Curators of the CIP; CIP 107957

#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 limicola strain DSM 15094

Flavobacterium limicola DSM 15094

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Change proposal