Name: Flavobacterium denitrificans ED5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5539

Type strain:

Species: Flavobacterium denitrificans

Strain Designation: ED5

Culture col. no.: DSM 15936, ATCC BAA-842, CIP 109214

Strain history: CIP <- 2006, DSMZ

NCBI tax ID(s): 1121888 (strain), 281361 (species)

SI-ID 138984

ATCC BAA-842, DSM 15936, CIP 109214

Other strains from Flavobacterium denitrificans

F. denitrificans CCUG 1818, CCM 1950, LMG 4016

Section

Flavobacterium denitrificans ED5 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from earthworm gut.

Gram-negative
motile
rod-shaped
facultative aerobe
mesophilic
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 denitrificans**
	Full Scientific Name (LPSN)	Flavobacterium denitrificans Horn et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31407]	Gram stain	negative
[Ref.: #118896]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #31407]	Cell length	1.6 µm

[Ref.: #31407]	Cell width	0.6 µm

[Ref.: #31407]	Cell shape	rod-shaped
[Ref.: #118896]	Cell shape	rod-shaped

[Ref.: #31407]	Motility	yes
[Ref.: #118896]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6195]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #6195]

Culture medium growth

[Ref.: #6195]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6195]

Culture medium composition

expand / minimize

[Ref.: #42255]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #42255]

Culture medium growth

[Ref.: #42255]

Culture medium composition

expand / minimize

[Ref.: #118896]

Culture medium

CIP Medium 72

[Ref.: #118896]

Culture medium growth

[Ref.: #118896]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #6195]	growth	25 °C
[Ref.: #31407]	growth	10-30 °C
[Ref.: #31407]	optimum	25 °C
[Ref.: #42255]	growth	25 °C

[Ref.: #6195]	Temperature range	mesophilic
[Ref.: #31407]	Temperature range	mesophilic
[Ref.: #42255]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31407]			optimum	7
[Ref.: #31407]			growth	5.5-8.2

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31407]	Oxygen tolerance	facultative aerobe
[Ref.: #118896]	Oxygen tolerance	obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31407]	arabinose ChEBI	+	carbon source
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31407]	cellobiose ChEBI	+	carbon source
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31407]	fructose ChEBI	+	carbon source
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31407]	gelatin ChEBI	+	carbon source
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31407]	glucose ChEBI	+	carbon source
[Ref.: #31407]	glutamate ChEBI	+	carbon source
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31407]	lactose ChEBI	+	carbon source
[Ref.: #31407]	maltose ChEBI	+	carbon source
[Ref.: #31407]	mannitol ChEBI	+	carbon source
[Ref.: #31407]	mannose ChEBI	+	carbon source
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31407]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31407]	nitrate ChEBI	+	reduction
[Ref.: #118896]	nitrate ChEBI	+	reduction
[Ref.: #118896]	nitrite ChEBI	+	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31407]	succinate ChEBI	+	carbon source
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31407]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #118896]		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.: #118896]	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.: #118896]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #118896]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

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

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #118896]	11495	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.: #118896]	11724	-	+	+	+	-	+	+	-	-	-	+	+	-	+	-	+	-	+	-	+

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

[Ref.: #6195]	Sample type/isolated from	earthworm (Aporectodea caliginosa) gut
[Ref.: #6195]	Host species	Aporrectodea caliginosa
[Ref.: #6195]	Geographic location (country and/or sea, region)	Bavaria, Bayreuth
[Ref.: #6195]	Country	Germany
[Ref.: #6195]	Country ISO 3 Code	DEU
[Ref.: #6195]	Continent	Europe

[Ref.: #118896]	Sample type/isolated from	Gut of the earthworn Aporrectodae caliginosa
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Annelida

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ318907 (>99% sequence identity) for Flavobacterium from Microbeatlas

Aquatic Samples	2
Soil Samples	17
Animal Samples
Plant Samples	2
Total Samples	21

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

[Ref.: #6195]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118896]	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.: #31407]	Flavobacterium denitrificans partial 16S rRNA gene, type strain ED5T	AJ318907	1447	GenBank	281361 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Flavobacterium denitrificans DSM 15936	GCA_000425445	scaffold	GenBank	1121888 tax ID	*
[Ref.: #66792]	Flavobacterium denitrificans DSM 15936	1121888.3	wgs	PATRIC	1121888 tax ID	*
[Ref.: #66792]	Flavobacterium denitrificans DSM 15936	2523533577	draft	JGI IMG/M	1121888 tax ID	*

[Ref.: #6195]

GC-content

34.6 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Flavobacterium denitrificans DSM 15936 DSM 15936 NCBI: GCA_000425445.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Flavobacterium denitrificans DSM 15936 DSM 15936 NCBI: GCA_000425445.1
[Ref.: #69480]	motile	no	80.096	yes
[Ref.: #69480]	flagellated	no	94.893	no
[Ref.: #69480]	gram-positive	no	98.494	no
[Ref.: #69480]	anaerobic	no	99.621	no
[Ref.: #69480]	aerobic	yes	89.596	yes
[Ref.: #69480]	halophile	no	95.938	no
[Ref.: #69480]	spore-forming	no	94.202	no
[Ref.: #69480]	thermophile	no	99.581	no
[Ref.: #69480]	glucose-util	yes	91.698	yes
[Ref.: #69480]	glucose-ferment	no	89.598	no

Availability in culture collections External links

[Ref.: #6195]

Culture collection no.

DSM 15936, ATCC BAA-842, CIP 109214

[Ref.: #75022]

SI-ID 138984

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavobacterium effusum sp. nov., isolated from a freshwater river.	Chen WM, Su CL, Kwon SW, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijsem.0.002944	2018	*
Phylogeny	Flavobacterium dispersum sp. nov., isolated from a freshwater spring.	Chen WM, Su CL, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijsem.0.002305	2017	*
Phylogeny	Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov., Paenibacillus anaericanus sp. nov. and Paenibacillus terrae strain MH72, N2O-producing bacteria isolated from the gut of the earthworm Aporrectodea caliginosa.	Horn MA, Ihssen J, Matthies C, Schramm A, Acker G, Drake HL	Int J Syst Evol Microbiol	10.1099/ijs.0.63484-0	2005	*

References

#6195

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15936

#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 )

#31407

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 #27716 (see below)

#42255 ; 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) .

#68371

Automatically annotated from API 50CH acid .

#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 )

#75022

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-ID138984.1 )

#118896 Collection of Institut Pasteur ; Curators of the CIP; CIP 109214

#27716

IJSEM 1255 2005 ( DOI 10.1099/ijs.0.63484-0 , PubMed 15879265 )

* These data were automatically processed and therefore are not curated

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Flavobacterium denitrificans DSM 15936 DSM 15936

Flavobacterium denitrificans DSM 15936 DSM 15936

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