Flavobacterium cucumis (DSM 18830, CIP 109888, KACC 11732)

Name: Flavobacterium cucumis (DSM 18830, CIP 109888, KACC 11732)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5565

Type strain

Strain Designation R2A45-3

Culture col. no. DSM 18830 CIP 109888 KACC 11732 R2A45-3

NCBI tax ID(s) 416016

Special Collections DSMZ CIP Literature strains

History <- S.-W. Kwon, KACC; R2A45-3 <- H.-Y. Weon et al., Natl. Inst. Agricult. Sci. and Technol., Suwon, Korea CIP <- 2008, DSMZ <- H.Y. Weon, Nat. Inst. Agr. Science & Tech., Suwon, Korea: strain 18830

Links

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

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

Name and taxonomic classification

SI-ID 309451

DSM 18830,KACC 11732,CIP 109888

@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 cucumis

Full scientific name Flavobacterium cucumis Weon et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
32083	negative	2.5 µm	0.5 µm	rod-shaped	gliding
118807	negative			rod-shaped
125438						94.5
125438	negative					97.75
125439	negative					99.8

Pigmentation

32083

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7727	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
33335	MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati		Distilled water make up to (1000.000 ml);R2A agar (18.200 g)
118807	CIP Medium 566	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7727	positive	growth	30
32083	positive	growth	05-37
32083	positive	optimum	30
33335	positive	growth	30

Culture pH

@ref	Ability	Type	PH
32083	positive	optimum	7
32083	positive	growth	06-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32083	aerobe
118807	obligate aerobe
125439	obligate aerobe	97.2

Spore formation

@ref	Spore formation	Confidence
32083
125438		94.765
125439		99

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32083	NaCl	positive	growth	0-2 %
32083	NaCl	positive	optimum	0-2 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32083	4853 ChEBI	esculin	+	hydrolysis
118807	17632 ChEBI	nitrate	-	reduction
118807	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118807	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
32083	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
32083	alkaline phosphatase	+	3.1.3.1
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
32083	alpha-galactosidase	+	3.2.1.22
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
32083	catalase	+	1.11.1.6
118807	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
32083	cytochrome oxidase	+	1.9.3.1
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
118807	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
118807	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
118807	-	+	+	+	-	+	+	+	+	+	+	+	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Greenhouse
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
7727	greenhouse soil cultivated with cucumber	Sangju region	Republic of Korea	KOR	Asia
118807	Environment, Greenhouse soils	Suwon	Republic of Korea	KOR	Asia	2007

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7727	1	Risk group (German classification) According to TRBA 466
118807	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	IMG-taxon 2698536819 annotated assembly for Flavobacterium cucumis DSM 18830	contig	GCA_900148835	416016.4	2698536819	416016	77.09

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7727	Flavobacterium cucumis strain R2A45-3 16S ribosomal RNA gene, partial sequence	EF126993	1439		416016

GC content

@ref	GC-content (mol%)
7727	38.0
32083	38

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Flavobacterium cucumis DSM 18830
NCBI: GCA_900148835

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.00	no
125439	motility	BacteriaNetⓘ	no	67.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Flavobacterium cucumis strain DSM 18830
PATRIC: 416016.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.75	no
125438	anaerobic	anaerobicⓘ	no	95.41	no
125438	spore-forming	spore-formingⓘ	no	94.77	yes
125438	aerobic	aerobicⓘ	yes	85.68	no
125438	thermophilic	thermophileⓘ	no	96.86	yes
125438	flagellated	motile2+ⓘ	no	94.50	yes

Literature

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 )
#28329	IJSEM 1594 2007 ( DOI 10.1099/ijs.0.64935-0 , PubMed 17625200 )
#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
#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 .
#118807	Collection of Institut Pasteur ; Curators of the CIP; CIP 109888
#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 cucumis (DSM 18830, CIP 109888, KACC 11732)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900148835

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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