Name: Flavobacterium filum EMB 34
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5569

Type strain:

Species: Flavobacterium filum

Strain Designation: EMB 34, EMB34

Culture col. no.: DSM 17961, KCTC 12610, CIP 109743

Strain history: CIP <- 2007, KCTC <- C.O. Jeon, Korea Univ., Seoul, Korea: strain EMB34

NCBI tax ID(s): 1121889 (strain), 370974 (species)

SI-ID 309532

DSM 17961, KCTC 12610, LMG 24723, CIP 109743

Special Collections

Section

Flavobacterium filum EMB 34 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from activated sludge.

Gram-negative
rod-shaped
facultative anaerobe
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Flavobacterium*
	Species	**Flavobacterium filum**
	Full Scientific Name (LPSN)	Flavobacterium filum Ryu et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32214]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #119349]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.5

[Ref.: #32214]	Cell length	1.55 µm

[Ref.: #32214]	Cell width	0.55 µm

[Ref.: #32214]	Cell shape	rod-shaped
[Ref.: #119349]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #32214]	Motility	no
[Ref.: #119349]	Motility	no
[Ref.: #67771]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %94

[Ref.: #32214]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7293]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7293]

Culture medium growth

[Ref.: #7293]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7293]

Culture medium composition

expand / minimize

[Ref.: #37833]

Culture medium

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

[Ref.: #37833]

Culture medium growth

[Ref.: #37833]

Culture medium composition

expand / minimize

[Ref.: #119349]

Culture medium

CIP Medium 566

[Ref.: #119349]

Culture medium growth

[Ref.: #119349]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7293]	growth	25 °C
[Ref.: #32214]	growth	10-40 °C
[Ref.: #32214]	optimum	30 °C
[Ref.: #37833]	growth	30 °C
[Ref.: #67771]	growth	25-32 °C

	pH	Kind of pH		pH
[Ref.: #32214]			optimum	7.75
[Ref.: #32214]			growth	6.0-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32214]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #119349]	Oxygen tolerance	obligate aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %93.833
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32214]		NaCl		growth	<2	%

[Ref.: #32214]	Observation	aggregates in clumps
[Ref.: #67771]	Observation	quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32214]	glucose ChEBI	+	carbon source
[Ref.: #32214]	lactose ChEBI	+	carbon source
[Ref.: #32214]	melibiose ChEBI	+	carbon source
[Ref.: #32214]	myo-inositol ChEBI	+	carbon source
[Ref.: #32214]	nitrate ChEBI	+	reduction
[Ref.: #119349]	nitrate ChEBI	+	reduction
[Ref.: #119349]	nitrite ChEBI	-	reduction
[Ref.: #32214]	raffinose ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #119349]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #32214]	alkaline phosphatase	+	3.1.3.1
[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.: #32214]	catalase	+	1.11.1.6
[Ref.: #119349]	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.: #119349]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #119349]	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.: #119349]	12080	-	+	+	+	-	+	+	-	+	-	+	+	-	-	-	+	-	+	-	-

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

[Ref.: #7293]	Sample type/isolated from	activated sludge
[Ref.: #7293]	Geographic location (country and/or sea, region)	Pohang
[Ref.: #7293]	Country	Republic of Korea
[Ref.: #7293]	Country ISO 3 Code	KOR
[Ref.: #7293]	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.: #119349]	Sample type/isolated from	Environment, Wastewater, treatment plant, that performed enhanced biological phosphorus removal
[Ref.: #119349]	Geographic location (country and/or sea, region)	Seoul
[Ref.: #119349]	Country	Republic of Korea
[Ref.: #119349]	Country ISO 3 Code	KOR
[Ref.: #119349]	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 DQ372981 (>99% sequence identity) for Flavobacterium filum subclade from Microbeatlas

Aquatic Samples	18
Soil Samples
Animal Samples	2
Plant Samples
Total Samples	20

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

[Ref.: #7293]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119349]	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.: #7293]	Flavobacterium filum strain EMB34 16S ribosomal RNA gene, partial sequence	DQ372981	1436	GenBank ENA	1121889 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Flavobacterium filum DSM 17961	GCA_000425465	scaffold	GenBank ENA	1121889 tax ID	*
[Ref.: #66792]	Flavobacterium filum DSM 17961	1121889.3	wgs	PATRIC	1121889 tax ID	*
[Ref.: #66792]	Flavobacterium filum DSM 17961	2523533606	draft	JGI IMG/M	1121889 tax ID	*

[Ref.: #7293]	GC-content	34.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32214]	GC-content	34.2 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Flavobacterium filum DSM 17961 DSM 17961 NCBI: GCA_000425465.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Flavobacterium filum DSM 17961 DSM 17961 NCBI: GCA_000425465.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.5	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	93.44	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	81.772	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	93.833	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.451	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	94	no

Availability in culture collections External links

[Ref.: #7293]

Culture collection no.

DSM 17961, KCTC 12610, CIP 109743

[Ref.: #75052]

SI-ID 309532

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavobacterium lacus sp. nov., isolated from a high-altitude lake, and emended description of Flavobacterium filum.	Li A, Liu H, Sun B, Zhou Y, Xin Y	Int J Syst Evol Microbiol	10.1099/ijs.0.056689-0	2013	*
Phylogeny	Flavobacterium filum sp. nov., isolated from a wastewater treatment plant in Korea.	Ryu SH, Park M, Jeon Y, Lee JR, Park W, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.65138-0	2007	*

References

#7293

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17961

#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 )

#32214

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 #28456 (see below)

#37833 ; 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) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75052

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-ID309532.1 )

#119349 Collection of Institut Pasteur ; Curators of the CIP; CIP 109743

#28456

IJSEM 2026 2007 ( DOI 10.1099/ijs.0.65138-0 , PubMed 17766867 )

* These data were automatically processed and therefore are not curated

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Flavobacterium filum DSM 17961 DSM 17961

Flavobacterium filum DSM 17961 DSM 17961

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