Name: Flavobacterium croceum EMB 47
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5562

Type strain:

Species: Flavobacterium croceum

Strain Designation: EMB 47, EMB47

Culture col. no.: DSM 17960, CIP 109940, KCTC 12611

Strain history: CIP <- 2009, DSMZ <- C.O. Jeon, GSNU, Jinju, Korea: strain EMB47

NCBI tax ID(s): 1121886 (strain), 370975 (species)

SI-ID 297163

DSM 17960, KCTC 12611, CIP 109940

Special Collections

Section

When using BacDive for research please cite our paper

Flavobacterium croceum EMB 47 is an aerobe, mesophilic, rod-shaped bacterium that was isolated from activated sludge.

rod-shaped
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Flavobacterium*
	Species	**Flavobacterium croceum**
	Full Scientific Name (LPSN)	Flavobacterium croceum Park et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #118789]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.8
[Ref.: #125438]	Gram stain	negative Confidence in %99

[Ref.: #118789]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #118789]	Motility	no
[Ref.: #67771]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %94.5

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7292]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7292]

Culture medium growth

[Ref.: #7292]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7292]

Culture medium composition

expand / minimize

[Ref.: #41934]

Culture medium

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

[Ref.: #41934]

Culture medium growth

[Ref.: #41934]

Culture medium composition

expand / minimize

[Ref.: #118789]

Culture medium

CIP Medium 566

[Ref.: #118789]

Culture medium growth

[Ref.: #118789]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7292]	growth	25 °C
[Ref.: #41934]	growth	25 °C
[Ref.: #67771]	growth	25-32 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #118789]	Oxygen tolerance	facultative anaerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %96.5

[Ref.: #125439]	Ability of spore formation	no Confidence in %99.4
[Ref.: #125438]	Ability of spore formation	no Confidence in %92.687

[Ref.: #67771]

Observation

quinones: MK-6

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #118789]		nitrate ChEBI	+	reduction
[Ref.: #118789]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #118789]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[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.: #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.: #118789]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[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.: #118789]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #118789]	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.: #118789]	12236	-	+	+	+	-	+	+	+	+	-	+	+	-	-	-	+	-	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	purine metabolism	63.83	60 of 94
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	phenylalanine metabolism	61.54	8 of 13
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	heme metabolism	50	7 of 14
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	histidine metabolism	44.83	13 of 29
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	oxidative phosphorylation	40.66	37 of 91
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	proline metabolism	36.36	4 of 11
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	arginine metabolism	29.17	7 of 24
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	25	3 of 12
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	valine metabolism	22.22	2 of 9
[Ref.: #66794]	degradation of pentoses	21.43	6 of 28
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #7292]	Sample type/isolated from	activated sludge
[Ref.: #7292]	Geographic location (country and/or sea, region)	Pohang
[Ref.: #7292]	Country	Republic of Korea
[Ref.: #7292]	Country ISO 3 Code	KOR
[Ref.: #7292]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From activated sludge
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #118789]	Sample type/isolated from	Environment, Activated sludge
[Ref.: #118789]	Geographic location (country and/or sea, region)	Pohang
[Ref.: #118789]	Country	Republic of Korea
[Ref.: #118789]	Country ISO 3 Code	KOR
[Ref.: #118789]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Activated sludge

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ372982 (>99% sequence identity) for Flavobacterium croceum subclade from Microbeatlas

Aquatic Samples	673
Soil Samples	19
Animal Samples	27
Plant Samples	24
Total Samples	743

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

[Ref.: #7292]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118789]	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.: #7292]	Flavobacterium croceum strain EMB47 16S ribosomal RNA gene, partial sequence	DQ372982	1439	GenBank ENA	370975 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Flavobacterium croceum DSM 17960	GCA_002917885	contig	GenBank ENA	1121886 tax ID	*
[Ref.: #66792]	Flavobacterium croceum DSM 17960	1121886.3	wgs	PATRIC	1121886 tax ID	*
[Ref.: #66792]	Flavobacterium croceum DSM 17960	2734482249	draft	JGI IMG/M	1121886 tax ID	*

[Ref.: #7292]	GC-content	40.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	40.8 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Flavobacterium croceum DSM 17960 PATRIC: 1121886.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	99	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.795	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	92.687	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	81.811	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	92.131	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	94.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Flavobacterium croceum DSM 17960 NCBI: GCA_002917885
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.4
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	69.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.8
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	96.5

Availability in culture collections External links

[Ref.: #7292]

Culture collection no.

DSM 17960, CIP 109940, KCTC 12611

[Ref.: #75044]

SI-ID 297163

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavobacterium croceum sp. nov., isolated from activated sludge.	Park M, Lu S, Ryu SH, Chung BS, Park W, Kim CJ, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.64436-0	2006	*

References

#7292

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17960

#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 )

#41934 ; 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) .

#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 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#75044

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-ID297163.1 )

#118789 Collection of Institut Pasteur ; Curators of the CIP; CIP 109940

#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 .

* These data were automatically processed and therefore are not curated

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Flavobacterium croceum DSM 17960

Flavobacterium croceum DSM 17960

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Change proposal