Flavobacterium rivuli (DSM 21788, CIP 109865, CCUG 58934)

Name: Flavobacterium rivuli (DSM 21788, CIP 109865, CCUG 58934)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5575

Type strain

Strain Designation WB3.3-2

Culture col. no. DSM 21788 CIP 109865 CCUG 58934 WB3.3-2 WB 3.3-2

NCBI tax ID(s) 1121895 498301

Special Collections DSMZ CCUG CIP Literature strains

Links

Flavobacterium rivuli WB3.3-2 is an aerobe, psychrophilic, Gram-negative prokaryote that was isolated from water of a hardwater creek.

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

Name and taxonomic classification

SI-ID 363443

DSM 21788,CIP 109865,LMG 25807,CCUG 58934

@ref 20215

Last LPSN update 2025-12-16 09:48:06

Domain Pseudomonadati

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Flavobacterium

Species Flavobacterium rivuli

Full scientific name Flavobacterium rivuli Ali et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29215	negative	2 µm	0.5 µm	rod-shaped
122243	negative			rod-shaped
125438					91
125438	negative				97.196
125439	negative				99.9

Colony morphology

61780

Incubation period1-2 days

Pigmentation

29215

Productionno

Multimedia

@ref:	66793
multimedia content:	EM_DSM_21788_1.jpg
multimedia.multimedia content:	EM_DSM_21788_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_21788_2.jpg
multimedia.multimedia content:	EM_DSM_21788_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_21788_3.jpg
multimedia.multimedia content:	EM_DSM_21788_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_21788_4.jpg
multimedia.multimedia content:	EM_DSM_21788_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_21788_5.jpg
multimedia.multimedia content:	EM_DSM_21788_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_21788_6.jpg
multimedia.multimedia content:	EM_DSM_21788_6.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15951	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
42068	MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati		Distilled water make up to (1000.000 ml);R2A agar (18.200 g)
122243	CIP Medium 566	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15951	positive	growth	20	psychrophilic
29215	positive	growth	04-29
29215	positive	optimum	16-24	psychrophilic
42068	positive	growth	25	mesophilic
61780	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
29215	positive	optimum	7
29215	positive	growth	6.4-7.8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29215	aerobe
61780	aerobe
122243	obligate aerobe
125439	obligate aerobe	94.1

Spore formation

@ref	Spore formation	Confidence
125439		99.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29215	NaCl	positive	growth	0-2 %
29215	NaCl	positive	optimum	1 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29215	30089 ChEBI	acetate	+	carbon source
29215	22599 ChEBI	arabinose	+	carbon source
29215	17057 ChEBI	cellobiose	+	carbon source
29215	4853 ChEBI	esculin	+	hydrolysis
29215	28757 ChEBI	fructose	+	carbon source
29215	28260 ChEBI	galactose	+	carbon source
29215	17234 ChEBI	glucose	+	carbon source
29215	17716 ChEBI	lactose	+	carbon source
29215	17306 ChEBI	maltose	+	carbon source
29215	37684 ChEBI	mannose	+	carbon source
29215	28053 ChEBI	melibiose	+	carbon source
29215	51850 ChEBI	methyl pyruvate	+	carbon source
122243	17632 ChEBI	nitrate	-	reduction
122243	16301 ChEBI	nitrite	-	reduction
29215	26271 ChEBI	proline	+	carbon source
29215	26986 ChEBI	threonine	+	carbon source
29215	27082 ChEBI	trehalose	+	carbon source
29215	53423 ChEBI	tween 40	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29215	16136 ChEBI	hydrogen sulfide
122243	35581 ChEBI	indole

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
29215	catalase	+	1.11.1.6
122243	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
29215	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
122243	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
122243	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	kanosamine biosynthesis II	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	biotin biosynthesis	100	4 of 4
66794	CMP-KDO biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	enterobactin biosynthesis	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	ribulose monophosphate pathway	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	glycine betaine biosynthesis	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	valine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	pentose phosphate pathway	81.82	9 of 11
66794	starch degradation	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	butanoate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	degradation of sugar alcohols	75	12 of 16
66794	glycogen biosynthesis	75	3 of 4
66794	purine metabolism	74.47	70 of 94
66794	methionine metabolism	73.08	19 of 26
66794	NAD metabolism	72.22	13 of 18
66794	propanol degradation	71.43	5 of 7
66794	leucine metabolism	69.23	9 of 13
66794	histidine metabolism	68.97	20 of 29
66794	lipid metabolism	67.74	21 of 31
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	pyrimidine metabolism	66.67	30 of 45
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	glycolysis	64.71	11 of 17
66794	citric acid cycle	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	phenylalanine metabolism	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of hexoses	61.11	11 of 18
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	glycogen metabolism	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	heme metabolism	57.14	8 of 14
66794	tyrosine metabolism	57.14	8 of 14
66794	degradation of pentoses	57.14	16 of 28
66794	lysine metabolism	57.14	24 of 42
66794	degradation of sugar acids	56	14 of 25
66794	molybdenum cofactor biosynthesis	55.56	5 of 9
66794	tryptophan metabolism	55.26	21 of 38
66794	isoprenoid biosynthesis	50	13 of 26
66794	suberin monomers biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	proline metabolism	45.45	5 of 11
66794	metabolism of disaccharids	45.45	5 of 11
66794	carotenoid biosynthesis	45.45	10 of 22
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	glutathione metabolism	42.86	6 of 14
66794	oxidative phosphorylation	42.86	39 of 91
66794	mevalonate metabolism	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	3-chlorocatechol degradation	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	myo-inositol biosynthesis	40	4 of 10
66794	gallate degradation	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	sulfate reduction	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	ketogluconate metabolism	37.5	3 of 8
66794	arginine metabolism	37.5	9 of 24
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	octane oxidation	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	sphingosine metabolism	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	urea cycle	30.77	4 of 13
66794	glycine metabolism	30	3 of 10
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	polyamine pathway	26.09	6 of 23
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	daunorubicin biosynthesis	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9

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
122243	-	+	-	+	-	+	+	-	-	-	+	+	+	+	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#River (Creek)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15951	water of a hardwater creek	Harz Mountains, Westerhöfer Bach, Westerhof, 40 km north of Göttingen	Germany	DEU	Europe
61780	Water,hardwater creek	Westerhof,Harz Mountains	Germany	DEU	Europe
122243	Environment, Hard water, river	Westerhöfer Bach, Harz mountains	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence AM934661 (>99% sequence identity) for Flavobacterium from Microbeatlas

Aquatic Samples	1682
Soil Samples	370
Animal Samples	1194
Plant Samples	195
Total Samples	3441

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15951	1	Risk group (German classification) According to TRBA 466
122243	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	ASM37848v1 assembly for Flavobacterium rivuli WB 3.3-2 = DSM 21788	scaffold	GCA_000378485	1121895.5	2519103183	1121895	74.44
66792	ASM76982v1 assembly for Flavobacterium rivuli WB 3.3-2 = DSM 21788	contig	GCA_000769825	1121895.7	2636415943	1121895	67.09

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15951	Flavobacterium rivuli partial 16S rRNA gene, type strain WB3.3-2T	AM934661	1488		498301

GC content

@ref	GC-content (mol%)	Method
15951	40.4	high performance liquid chromatography (HPLC)
29215	40.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Flavobacterium rivuli WB 3.3-2 = DSM 21788
NCBI: GCA_000378485

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	motility	BacteriaNetⓘ	no	75.50	no
125439	spore_formation	BacteriaNetⓘ	no	99.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Flavobacterium rivuli WB 3.3-2 = DSM 21788 DSM 21788
NCBI: GCA_000378485.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.20	yes
125438	anaerobic	anaerobicⓘ	no	96.54	yes
125438	aerobic	aerobicⓘ	yes	87.80	yes
125438	spore-forming	spore-formingⓘ	no	85.79	no
125438	thermophilic	thermophileⓘ	no	94.89	yes
125438	flagellated	motile2+ⓘ	no	91.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Comparative genomic analysis indicates that niche adaptation of terrestrial Flavobacteria is strongly linked to plant glycan metabolism.	Kolton M, Sela N, Elad Y, Cytryn E.	PLoS One	10.1371/journal.pone.0076704	2013
Genetics	High quality draft genomic sequence of Flavobacterium enshiense DK69(T) and comparison among Flavobacterium genomes.	Zeng Z, Chen C, Du H, Wang G, Li M.	Stand Genomic Sci	10.1186/s40793-015-0084-z	2015
Genetics	High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes.	Hahnke RL, Stackebrandt E, Meier-Kolthoff JP, Tindall BJ, Huang S, Rohde M, Lapidus A, Han J, Trong S, Haynes M, Reddy TB, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Markowitz V, Woyke T, Goker M, Kyrpides NC, Klenk HP	Stand Genomic Sci	10.1186/s40793-015-0032-y	2015
Phylogeny	Flavobacterium hauense sp. nov., isolated from soil and emended descriptions of Flavobacterium subsaxonicum, Flavobacterium beibuense and Flavobacterium rivuli.	Dong K, Xu B, Zhu F, Wang G.	Int J Syst Evol Microbiol	10.1099/ijs.0.048652-0	2013
Phylogeny	Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai'i, and emended description of the genus Flavobacterium.	Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY, Donachie SP.	Int J Syst Evol Microbiol	10.1099/ijs.0.047217-0	2013
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

#15951	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21788
#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 )
#29215	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 #25636 (see below)
#42068	; Curators of the CIP;
#61780	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 58934
#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) .
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#122243	Collection of Institut Pasteur ; Curators of the CIP; CIP 109865
#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 rivuli (DSM 21788, CIP 109865, CCUG 58934)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000378485

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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