Name: Flavobacterium cucumis R2A45-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5565

Type strain:

Species: Flavobacterium cucumis

Strain Designation: R2A45-3

Culture col. no.: DSM 18830, CIP 109888, KACC 11732

Strain history: CIP <- 2008, DSMZ <- H.Y. Weon, Nat. Inst. Agr. Science & Tech., Suwon, Korea: strain 18830

NCBI tax ID(s): 416016 (species)

SI-ID 309451

DSM 18830, KACC 11732, CIP 109888

Section

Flavobacterium cucumis R2A45-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from greenhouse soil cultivated with cucumber.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Flavobacterium*
	Species	**Flavobacterium cucumis**
	Full Scientific Name (LPSN)	Flavobacterium cucumis Weon et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32083]	Gram stain	negative
[Ref.: #118807]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #32083]	Cell length	2.5 µm

[Ref.: #32083]	Cell width	0.5 µm

[Ref.: #32083]	Cell shape	rod-shaped
[Ref.: #118807]	Cell shape	rod-shaped

[Ref.: #32083]	Motility	yes
[Ref.: #118807]	Motility	no

[Ref.: #32083]	Flagellum arrangement	gliding

[Ref.: #32083]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7727]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7727]

Culture medium growth

[Ref.: #7727]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7727]

Culture medium composition

expand / minimize

[Ref.: #33335]

Culture medium

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

[Ref.: #33335]

Culture medium growth

[Ref.: #33335]

Culture medium composition

expand / minimize

[Ref.: #118807]

Culture medium

CIP Medium 566

[Ref.: #118807]

Culture medium growth

[Ref.: #118807]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7727]	growth	30 °C
[Ref.: #32083]	growth	05-37 °C
[Ref.: #32083]	optimum	30 °C
[Ref.: #33335]	growth	30 °C

[Ref.: #7727]	Temperature range	mesophilic
[Ref.: #32083]	Temperature range	mesophilic
[Ref.: #33335]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32083]			optimum	7
[Ref.: #32083]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32083]	Oxygen tolerance	aerobe
[Ref.: #118807]	Oxygen tolerance	obligate aerobe

[Ref.: #32083]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32083]		NaCl		growth	0-2	%
[Ref.: #32083]		NaCl		optimum	0-2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32083]	esculin ChEBI	+	hydrolysis
[Ref.: #118807]	nitrate ChEBI	-	reduction
[Ref.: #118807]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #118807]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #32083]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #32083]	alkaline phosphatase	+	3.1.3.1
[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.: #32083]	alpha-galactosidase	+	3.2.1.22
[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.: #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.: #32083]	catalase	+	1.11.1.6
[Ref.: #118807]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #32083]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118807]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #118807]	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.: #118807]	12194	-	+	+	+	-	+	+	+	+	+	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #7727]	Sample type/isolated from	greenhouse soil cultivated with cucumber
[Ref.: #7727]	Geographic location (country and/or sea, region)	Sangju region
[Ref.: #7727]	Country	Republic of Korea
[Ref.: #7727]	Country ISO 3 Code	KOR
[Ref.: #7727]	Continent	Asia

[Ref.: #118807]	Sample type/isolated from	Environment, Greenhouse soils
[Ref.: #118807]	Geographic location (country and/or sea, region)	Suwon
[Ref.: #118807]	Country	Republic of Korea
[Ref.: #118807]	Country ISO 3 Code	KOR
[Ref.: #118807]	Continent	Asia
[Ref.: #118807]	Isolation date	2007
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Greenhouse
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF126993 (>99% sequence identity) for Flavobacterium from Microbeatlas

Aquatic Samples	2595
Soil Samples	257
Animal Samples	363
Plant Samples	30
Total Samples	3245

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

[Ref.: #7727]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118807]	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.: #7727]	Flavobacterium cucumis strain R2A45-3 16S ribosomal RNA gene, partial sequence	EF126993	1439	ENA	416016 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Flavobacterium cucumis DSM 18830	GCA_900148835	contig	GenBank	416016 tax ID	*
[Ref.: #66792]	Flavobacterium cucumis strain DSM 18830	416016.4	wgs	PATRIC	416016 tax ID	*
[Ref.: #66792]	Flavobacterium cucumis DSM 18830	2698536819	draft	JGI IMG/M	416016 tax ID	*

[Ref.: #7727]	GC-content	38.0 mol%
[Ref.: #32083]	GC-content	38 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Flavobacterium cucumis strain DSM 18830 PATRIC: 416016.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Flavobacterium cucumis strain DSM 18830 PATRIC: 416016.4
[Ref.: #69480]	gram-positive	no	98.916	no
[Ref.: #69480]	anaerobic	no	98.604	yes
[Ref.: #69480]	halophile	no	93.29	no
[Ref.: #69480]	spore-forming	no	95.501	no
[Ref.: #69480]	glucose-util	yes	84.901	no
[Ref.: #69480]	aerobic	yes	85.83	no
[Ref.: #69480]	flagellated	no	94.137	yes
[Ref.: #69480]	thermophile	no	98.247	no
[Ref.: #69480]	motile	no	89.818	no
[Ref.: #69480]	glucose-ferment	no	92.989	no

Availability in culture collections External links

[Ref.: #7727]

Culture collection no.

DSM 18830, CIP 109888, KACC 11732

[Ref.: #75047]

SI-ID 309451

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavobacterium proteolyticum sp. nov., isolated from aquaculture water.	Du J, Liu Y, Pei T, Li A, Deng MR, Zhu H	Arch Microbiol	10.1007/s00203-021-02744-2	2022	*
Phylogeny	Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil.	Kim I, Kim J, Chhetri G, Seo T	J Microbiol	10.1007/s12275-019-9350-x	2019	*
Phylogeny	Flavobacterium aquaticum sp. nov., isolated from a water sample of a rice field.	Subhash Y, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.050047-0	2013	*
Phylogeny	Flavobacterium sasangense sp. nov., isolated from a wastewater stream polluted with heavy metals.	Yoon HS, Aslam Z, Song GC, Kim SW, Jeon CO, Chon TS, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.004978-0	2009	*
Phylogeny	Flavobacterium cheniae sp. nov., isolated from sediment of a eutrophic reservoir.	Qu JH, Li HF, Yang JS, Yuan HL	Int J Syst Evol Microbiol	10.1099/ijs.0.65586-0	2008	*
Phylogeny	Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov., isolated from greenhouse soil.	Weon HY, Song MH, Son JA, Kim BY, Kwon SW, Go SJ, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.64935-0	2007	*
Phylogeny	Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead).	Kang S, Lee JY, Han JE, Jeong YS, Gim DH, Bae JW	J Microbiol	10.1007/s12275-022-2075-2	2022	*

References

#7727

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18830

#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 )

#32083

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 #28329 (see below)

#33335 ; 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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75047

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-ID309451.1 )

#118807 Collection of Institut Pasteur ; Curators of the CIP; CIP 109888

#28329

IJSEM 1594 2007 ( DOI 10.1099/ijs.0.64935-0 , PubMed 17625200 )

* These data were automatically processed and therefore are not curated

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Flavobacterium cucumis strain DSM 18830

Flavobacterium cucumis strain DSM 18830

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