Flavobacterium hercynium (DSM 18292, LMG 26768, WB4.2-33)

Name: Flavobacterium hercynium (DSM 18292, LMG 26768, WB4.2-33)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5568

Type strain

Strain Designation WB4.2-33

Culture col. no. DSM 18292 LMG 26768 WB4.2-33 CIP 109241 WB 4.2-33

NCBI tax ID(s) 387094

Special Collections DSMZ Literature strains CIP

History <- S. Cousin <- O. Päuker; WB4.2-33 CIP <- 2006, DSMZ <- O. Päuker: strain WB 4.2-33

Links

Flavobacterium hercynium WB4.2-33 is an aerobe, Gram-negative, motile bacterium that was isolated from stream water.

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

Name and taxonomic classification

SI-ID 297201

CIP 109241,DSM 18292,LMG 26768,CCUG 59448

@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 hercynium

Full scientific name Flavobacterium hercynium Cousin et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
31865	negative	5.8-6.3 µm	0.7-0.8 µm	rod-shaped	gliding
119882	negative			rod-shaped
125439	negative					99.5
125438						92
125438	negative					96.482

Pigmentation

31865

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7488	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
42257	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119882	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7488	positive	growth	25
31865	positive	growth	12-29
31865	positive	optimum	23.5
42257	positive	growth	25

Culture pH

@ref	Ability	Type	PH
31865	positive	optimum	7.1
31865	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31865	aerobe
119882	obligate aerobe
125439	obligate aerobe	97.3

Spore formation

@ref	Spore formation	Confidence
125439		98.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31865	NaCl	positive	growth	0-1 %
31865	NaCl	positive	optimum	0.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31865	40585 ChEBI	alpha-cyclodextrin	+	carbon source
31865	22653 ChEBI	asparagine	+	carbon source
31865	35391 ChEBI	aspartate	+	carbon source
31865	17057 ChEBI	cellobiose	+	carbon source
31865	16947 ChEBI	citrate	+	carbon source
31865	4853 ChEBI	esculin	+	hydrolysis
31865	28757 ChEBI	fructose	+	carbon source
31865	28260 ChEBI	galactose	+	carbon source
31865	28087 ChEBI	glycogen	+	carbon source
31865	18403 ChEBI	L-arabitol	+	carbon source
31865	17306 ChEBI	maltose	+	carbon source
31865	29864 ChEBI	mannitol	+	carbon source
31865	37684 ChEBI	mannose	+	carbon source
31865	37657 ChEBI	methyl D-glucoside	+	carbon source
31865	506227 ChEBI	N-acetylglucosamine	+	carbon source
31865	17632 ChEBI	nitrate	+	reduction
119882	17632 ChEBI	nitrate	+	reduction
119882	16301 ChEBI	nitrite	+	reduction
31865	18257 ChEBI	ornithine	+	carbon source
31865	53258 ChEBI	sodium citrate	+	carbon source
31865	26986 ChEBI	threonine	+	carbon source
31865	27082 ChEBI	trehalose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119882	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
31865	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
119882	alcohol dehydrogenase	-	1.1.1.1
31865	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
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
31865	catalase	+	1.11.1.6
119882	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31865	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
31865	gelatinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
119882	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119882	ornithine decarboxylase	-	4.1.1.17
119882	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
119882	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
119882	-	+	+	+	-	+	+	-	-	-	+	+	-	+	-	+	+	+	-	-

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	Isolation date
7488	stream water	Lower Saxony, Westhöfer Bach	Germany	DEU	Europe
119882	Environment, Hard water creek		Germany	DEU	Europe	2005

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7488	1	Risk group (German classification) According to TRBA 466
119882	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
124043	IMG-taxon 2724679814 annotated assembly for Flavobacterium hercynium DSM 18292	contig	GCA_900182755	387094.9	2724679814	387094	68.93
66792	ASM221728v1 assembly for Flavobacterium hercynium DSM 18292	scaffold	GCA_002217285	387094.4	8114409890	387094	57.45

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Flavobacterium hercynium strain DSM 18292 16S ribosomal RNA gene, partial sequence	JX657042	1223		387094
7488	Flavobacterium hercynium partial 16S rRNA gene, type strain WB 4.2-33T	AM265623	1502		387094

GC content

@ref	GC-content (mol%)	Method
7488	33.9	fluorimetric
31865	37.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Flavobacterium hercynium DSM 18292
NCBI: GCA_002217285

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.10	no
125439	motility	BacteriaNetⓘ	no	59.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Flavobacterium hercynium DSM 18292
NCBI: GCA_002217285.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.48	yes
125438	anaerobic	anaerobicⓘ	no	95.79	no
125438	aerobic	aerobicⓘ	yes	85.42	yes
125438	spore-forming	spore-formingⓘ	no	86.10	no
125438	thermophilic	thermophileⓘ	no	97.24	yes
125438	flagellated	motile2+ⓘ	no	92.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Calcite biomineralization by bacterial isolates from the recently discovered pristine karstic herrenberg cave.	Rusznyak A, Akob DM, Nietzsche S, Eusterhues K, Totsche KU, Neu TR, Frosch T, Popp J, Keiner R, Geletneky J, Katzschmann L, Schulze ED, Kusel K.	Appl Environ Microbiol	10.1128/aem.06568-11	2012
	Flavobacterium pygoscelis sp. nov., isolated from a chinstrap penguin chick (Pygoscelis antarcticus).	Irgang R, Poblete-Morales M, Avendano-Herrera R.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005815	2023
Phylogeny	Flavobacterium compostarboris sp. nov., isolated from leaf-and-branch compost, and emended descriptions of Flavobacterium hercynium, Flavobacterium resistens and Flavobacterium johnsoniae.	Kim JJ, Kanaya E, Weon HY, Koga Y, Takano K, Dunfield PF, Kwon SW, Kanaya S.	Int J Syst Evol Microbiol	10.1099/ijs.0.032920-0	2012
Phylogeny	Flavobacterium chilense sp. nov. and Flavobacterium araucananum sp. nov., isolated from farmed salmonid fish.	Kampfer P, Lodders N, Martin K, Avendano-Herrera R.	Int J Syst Evol Microbiol	10.1099/ijs.0.033431-0	2012
Phylogeny	Flavobacterium chungangense sp. nov., isolated from a freshwater lake.	Kim JH, Kim KY, Cha CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.007955-0	2009
Phylogeny	Flavobacterium aquidurense sp. nov. and Flavobacterium hercynium sp. nov., from a hard-water creek.	Cousin S, Pauker O, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.64556-0	2007

References

#7488	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18292
#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 )
#28125	IJSEM 243 2007 ( DOI 10.1099/ijs.0.64556-0 , PubMed 17267958 )
#31865	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 #28125
#42257	; 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 .
#119882	Collection of Institut Pasteur ; Curators of the CIP; CIP 109241
#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 .
#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 hercynium (DSM 18292, LMG 26768, WB4.2-33)

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

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900182755

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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