Name: Flavobacterium omnivorum ZF-8
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5555

Type strain:

Species: Flavobacterium omnivorum

Strain Designation: ZF-8

Culture col. no.: DSM 19742, AS 1.2747, JCM 11313, CGMCC 1.2747, CIP 108050, KCTC 12490

Strain history: CIP <- 2003, JCM <- 2001, F. Zhu: strain ZF-8

NCBI tax ID(s): 178355 (species)

SI-ID 88291

JCM11313, AS 1.2747, LMG 21986, CIP 108050, KCTC 12490, DSM 19742, CGMCC 1.2747

Special Collections

Section

Flavobacterium omnivorum ZF-8 is an obligate aerobe, Gram-negative bacterium that was isolated from frozen soil from the China No. 1 glacier.

Gram-negative
obligate aerobe
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 omnivorum**
	Full Scientific Name (LPSN)	Flavobacterium omnivorum Zhu et al. 2003

Information on morphological and physiological properties Morphology

[Ref.: #121418]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98

[Ref.: #121418]	Cell shape	rod-shaped

[Ref.: #121418]	Motility	no

[Ref.: #121418]	Pigment production	no
[Ref.: #121418]	Pigment name	Flexirubin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8276]

Culture medium

PYG MEDIUM (B) (DSMZ Medium 1139)

[Ref.: #8276]

Culture medium growth

[Ref.: #8276]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8276]

Culture medium composition

expand / minimize

[Ref.: #39767]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #39767]

Culture medium growth

[Ref.: #39767]

Culture medium composition

expand / minimize

[Ref.: #121418]

Culture medium

CIP Medium 566

[Ref.: #121418]

Culture medium growth

[Ref.: #121418]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #121418]

Culture medium

CIP Medium 469

[Ref.: #121418]

Culture medium growth

[Ref.: #121418]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #121418]

Culture medium

CIP Medium 72

[Ref.: #121418]

Culture medium growth

[Ref.: #121418]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #8276]		growth	11 °C
[Ref.: #39767]		growth	10 °C
[Ref.: #67770]		growth	11 °C
[Ref.: #121418]		growth	5-15 °C
[Ref.: #121418]	no	growth	25 °C
[Ref.: #121418]	no	growth	30 °C
[Ref.: #121418]	no	growth	37 °C
[Ref.: #121418]	no	growth	41 °C
[Ref.: #121418]	no	growth	45 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #121418]

Oxygen tolerance

obligate aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %92.785
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Salt	Tested relation		Salt conc.
[Ref.: #121418]	NaCl		growth	0	%
[Ref.: #121418]	NaCl	no	growth	2	%
[Ref.: #121418]	NaCl	no	growth	4	%
[Ref.: #121418]	NaCl	no	growth	6	%
[Ref.: #121418]	NaCl	no	growth	8	%
[Ref.: #121418]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #121418]	citrate ChEBI	-	carbon source
[Ref.: #121418]	esculin ChEBI	+	hydrolysis
[Ref.: #121418]	hippurate ChEBI	+	hydrolysis
[Ref.: #121418]	malonate ChEBI	-	assimilation
[Ref.: #121418]	nitrate ChEBI	-	builds gas from
[Ref.: #121418]	nitrate ChEBI	-	reduction
[Ref.: #121418]	nitrite ChEBI	-	builds gas from
[Ref.: #121418]	nitrite ChEBI	-	reduction
[Ref.: #121418]	tributyrin ChEBI	+	hydrolysis

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #121418]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #121418]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #121418]		acetoin ChEBI	-
[Ref.: #121418]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #121418]	alcohol dehydrogenase	-	1.1.1.1
[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.: #121418]	amylase	+
[Ref.: #121418]	beta-galactosidase	+	3.2.1.23
[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.: #121418]	caseinase	+	3.4.21.50
[Ref.: #121418]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #121418]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #121418]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #121418]	gelatinase	+/-
[Ref.: #121418]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #121418]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #121418]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #121418]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121418]	oxidase	-
[Ref.: #121418]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #121418]	tryptophan deaminase	-
[Ref.: #121418]	tween esterase	-
[Ref.: #121418]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #121418]	2560	not determinedn.d.	+	-	+	+	+	-	-	+	+	+	+	+	+	+	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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.: #121418]	10848	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #8276]	Sample type/isolated from	frozen soil from the China No. 1 glacier
[Ref.: #8276]	Geographic location (country and/or sea, region)	North-West China, Xinjiang province
[Ref.: #8276]	Country	China
[Ref.: #8276]	Country ISO 3 Code	CHN
[Ref.: #8276]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Frozen soil from the China No. 1 glacier (Xinjiang Province)

[Ref.: #121418]	Sample type/isolated from	Environment, Frozen soil from the China n°1 glacier
[Ref.: #121418]	Geographic location (country and/or sea, region)	Xinjiang
[Ref.: #121418]	Country	China
[Ref.: #121418]	Country ISO 3 Code	CHN
[Ref.: #121418]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Glacier
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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

[Ref.: #8276]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121418]	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.: #8276]	Flavobacterium omnivorum As1.2747 16S ribosomal RNA gene, partial sequence	AF433174	1466	GenBank ENA	178355 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Flavobacterium omnivorum CGMCC 1.2747	GCA_900099915	scaffold	GenBank ENA	178355 tax ID
[Ref.: #66792]	Flavobacterium omnivorum strain CGMCC 1.2747	178355.3	wgs	PATRIC	178355 tax ID	*
[Ref.: #66792]	Flavobacterium omnivorum CGMCC 1.2747	2617270789	draft	JGI IMG/M	178355 tax ID	*

[Ref.: #8276]

GC-content

35.2 mol%

thermal denaturation, midpoint method (Tm)

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 omnivorum CGMCC 1.2747 NCBI: GCA_900099915.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Flavobacterium omnivorum strain CGMCC 1.2747 PATRIC: 178355.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.567	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	92.785	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	86.932	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	99.034	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	89.5	no

Availability in culture collections External links

[Ref.: #8276]

Culture collection no.

DSM 19742, AS 1.2747, JCM 11313, CGMCC 1.2747, CIP 108050, KCTC 12490

[Ref.: #75037]

SI-ID 88291

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavobacterium xueshanense sp. nov. and Flavobacterium urumqiense sp. nov., two psychrophilic bacteria isolated from glacier ice.	Dong K, Liu H, Zhang J, Zhou Y, Xin Y	Int J Syst Evol Microbiol	10.1099/ijs.0.030049-0	2011	*
Phylogeny	Flavobacterium xinjiangense sp. nov. and Flavobacterium omnivorum sp. nov., novel psychrophiles from the China No. 1 glacier.	Zhu F, Wang S, Zhou P	Int J Syst Evol Microbiol	10.1099/ijs.0.02310-0	2003	*

References

#8276

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19742

#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 )

#39767 ; 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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68382

Automatically annotated from API zym .

#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 )

#75037

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-ID88291.1 )

#121418 Collection of Institut Pasteur ; Curators of the CIP; CIP 108050
* These data were automatically processed and therefore are not curated

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Flavobacterium omnivorum CGMCC 1.2747

Flavobacterium omnivorum strain CGMCC 1.2747

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