Flavobacterium fontis (DSM 25660, JCM 18212, KACC 16593)

Name: Flavobacterium fontis (DSM 25660, JCM 18212, KACC 16593)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24022

Type strain

Culture col. no. DSM 25660 JCM 18212 KACC 16593 MIC 3010

NCBI tax ID(s) 1124188

Special Collections DSMZ JCM Literature strains

Links

Flavobacterium fontis DSM 25660 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from fresh water pond.

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

Name and taxonomic classification

SI-ID 408227

JCM 18212,DSM 25660

@ref 20215

Last LPSN update 2025-12-16 09:52:46

Domain Pseudomonadati

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Flavobacterium

Species Flavobacterium fontis

Full scientific name Flavobacterium fontis Chun et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
30818	negative	rod-shaped
125438			94.5
125438	negative		98.5
125439	negative		99.8

Pigmentation

30818

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20569	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
20569	positive	growth	25	mesophilic
30818	positive	growth	15-42
30818	positive	optimum	25	mesophilic
67770	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH
30818	positive	optimum	6
30818	positive	growth	5.5-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30818	aerobe
125439	obligate aerobe	96.1

Spore formation

@ref	Spore formation	Confidence
125438		94.803
125439		99.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30818	NaCl	positive	optimum	0.5 %

Observation

30818

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30818	28644 ChEBI	2-oxopentanoate	+	carbon source
30818	23652 ChEBI	dextrin	+	carbon source
30818	4853 ChEBI	esculin	+	hydrolysis
30818	24148 ChEBI	galactonate	+	carbon source
30818	29987 ChEBI	glutamate	+	carbon source
30818	15428 ChEBI	glycine	+	carbon source
30818	28087 ChEBI	glycogen	+	carbon source
30818	21217 ChEBI	L-alaninamide	+	carbon source
30818	26271 ChEBI	proline	+	carbon source
30818	26546 ChEBI	rhamnose	+	carbon source
30818	53423 ChEBI	tween 40	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30818	cytochrome oxidase	+	1.9.3.1
30818	gelatinase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	starch degradation	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	citric acid cycle	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	tryptophan metabolism	71.05	27 of 38
66794	propionate fermentation	70	7 of 10
66794	purine metabolism	67.02	63 of 94
66794	formaldehyde oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	d-mannose degradation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	lysine metabolism	61.9	26 of 42
66794	methionine metabolism	61.54	16 of 26
66794	methylglyoxal degradation	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	glycolysis	58.82	10 of 17
66794	tyrosine metabolism	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	non-pathway related	55.26	21 of 38
66794	lipid metabolism	54.84	17 of 31
66794	glutamate and glutamine metabolism	53.57	15 of 28
66794	ethanol fermentation	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	isoprenoid biosynthesis	50	13 of 26
66794	isoleucine metabolism	50	4 of 8
66794	pantothenate biosynthesis	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	Entner Doudoroff pathway	50	5 of 10
66794	heme metabolism	50	7 of 14
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	vitamin B1 metabolism	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	carotenoid biosynthesis	45.45	10 of 22
66794	metabolism of disaccharids	45.45	5 of 11
66794	mevalonate metabolism	42.86	3 of 7
66794	glutathione metabolism	42.86	6 of 14
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	oxidative phosphorylation	39.56	36 of 91
66794	arginine metabolism	37.5	9 of 24
66794	pentose phosphate pathway	36.36	4 of 11
66794	proline metabolism	36.36	4 of 11
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	valine metabolism	33.33	3 of 9
66794	degradation of hexoses	33.33	6 of 18
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	myo-inositol biosynthesis	30	3 of 10
66794	ascorbate metabolism	27.27	6 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	degradation of pentoses	25	7 of 28
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	degradation of sugar acids	24	6 of 25
66794	urea cycle	23.08	3 of 13
66794	sulfate reduction	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	arachidonic acid metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Pond (small)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
20569	fresh water pond	Jeonju (35° 50' N 127° 07' E)	Republic of Korea	KOR	Asia	35.8333	127.117 35.8333/127.117
67770	Freshwater pond in Jeonju		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence JN873147 (>99% sequence identity) for Flavobacterium from Microbeatlas

Aquatic Samples	5359
Soil Samples	410
Animal Samples	496
Plant Samples	219
Total Samples	6484

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20569	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2695420946 annotated assembly for Flavobacterium fontis DSM 25660	contig	GCA_900129405	1124188.3	2695420946	1124188	71.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20569	Flavobacterium fontis strain MIC3010 16S ribosomal RNA gene, partial sequence	JN873147	1378		1124188

GC content

@ref	GC-content (mol%)	Method
20569	41.0	high performance liquid chromatography (HPLC)
30818	41

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Flavobacterium fontis DSM 25660
NCBI: GCA_900129405

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	no	72.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Flavobacterium fontis strain DSM 25660
PATRIC: 1124188.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	97.71	yes
125438	spore-forming	spore-formingⓘ	no	94.80	no
125438	aerobic	aerobicⓘ	yes	84.59	yes
125438	thermophilic	thermophileⓘ	no	96.11	yes
125438	flagellated	motile2+ⓘ	no	94.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavobacterium lutivivi sp. nov., isolated from activated sludge.	Feng Q, Han L, Nogi Y, Hong Q, Lv J	Int J Syst Evol Microbiol	10.1099/ijsem.0.000892	2016
Phylogeny	Flavobacterium fontis sp. nov., isolated from freshwater.	Chun J, Kang JY, Jahng KY	Int J Syst Evol Microbiol	10.1099/ijs.0.045203-0	2012
Phylogeny	Flavobacterium stagni sp. nov., isolated from a freshwater reservoir.	Chen WM, Guo YP, Kwon SW, Sheu C, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijsem.0.003488	2019

References

#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 )
#20569	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25660
#30818	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 #27149 (see below)
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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 fontis (DSM 25660, JCM 18212, KACC 16593)

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

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900129405

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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