Flavobacterium denitrificans (DSM 15936, ATCC BAA-842, CIP 109214)

Name: Flavobacterium denitrificans (DSM 15936, ATCC BAA-842, CIP 109214)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5539

Type strain

Strain Designation ED5

Culture col. no. DSM 15936 ATCC BAA-842 CIP 109214 ED5

NCBI tax ID(s) 1121888 281361

Special Collections DSMZ CIP Literature strains

History <- A. Schramm; ED5 <- J. Ihssen 2006, DSMZ CIP <- 2006, DSMZ

Links

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

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

Name and taxonomic classification

SI-ID 138984

ATCC BAA-842,DSM 15936,CIP 109214

@ref 20215

Last LPSN update 2026-02-09 11:18:59

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Flavobacterium

Species Flavobacterium denitrificans

Full scientific name Flavobacterium denitrificans Horn et al. 2005

BacDive ID	Other strains from **Flavobacterium denitrificans** (1)	Type strain
141432	F. denitrificans CCUG 1818, CCM 1950, LMG 4016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31407	negative	1.6 µm	0.6 µm	rod-shaped
118896	negative			rod-shaped
125438					93
125438	negative				97.682
125439	negative				99.9

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6195	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
42255	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118896	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6195	positive	growth	25	mesophilic
31407	positive	growth	10-30
31407	positive	optimum	25	mesophilic
42255	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH
31407	positive	optimum	7
31407	positive	growth	5.5-8.2

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31407	facultative aerobe
118896	obligate aerobe
125439	obligate aerobe	97.7

Spore formation

@ref	Spore formation	Confidence
125439		98.4

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31407	22599 ChEBI	arabinose	+	carbon source
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
31407	17057 ChEBI	cellobiose	+	carbon source
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
31407	28757 ChEBI	fructose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
31407	5291 ChEBI	gelatin	+	carbon source
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
31407	17234 ChEBI	glucose	+	carbon source
31407	29987 ChEBI	glutamate	+	carbon source
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
31407	17716 ChEBI	lactose	+	carbon source
31407	17306 ChEBI	maltose	+	carbon source
31407	29864 ChEBI	mannitol	+	carbon source
31407	37684 ChEBI	mannose	+	carbon source
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
31407	506227 ChEBI	N-acetylglucosamine	+	carbon source
31407	17632 ChEBI	nitrate	+	reduction
118896	17632 ChEBI	nitrate	+	reduction
118896	16301 ChEBI	nitrite	+	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
31407	30031 ChEBI	succinate	+	carbon source
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
31407	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118896	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	+	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
118896	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118896	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
118896	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
118896	-	+	+	+	-	+	+	-	-	-	+	+	-	+	-	+	-	+	-	+

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
118896	not determinedn.d.	-	-	-	+/-	-	+/-	-	-	-	+/-	+/-	-	+/-	-	-	-	-	-	-	-	-	+/-	+/-	-	+	-	+/-	+/-	+/-	-	-	-	-	-	-	+/-	+/-	-	+/-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Annelida

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
6195	earthworm (Aporectodea caliginosa) gut	Aporrectodea caliginosa	Bavaria, Bayreuth	Germany	DEU	Europe
118896	Gut of the earthworn Aporrectodae caliginosa

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6195	1	Risk group (German classification) According to TRBA 466
118896	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM42544v1 assembly for Flavobacterium denitrificans DSM 15936	scaffold	GCA_000425445	1121888.3	2523533577	1121888	73.48

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31407	Flavobacterium denitrificans partial 16S rRNA gene, type strain ED5T	AJ318907	1447		281361

GC content

6195

GC-content (mol%)34.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Flavobacterium denitrificans DSM 15936
NCBI: GCA_000425445

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.40	no
125439	motility	BacteriaNetⓘ	no	68.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Flavobacterium denitrificans DSM 15936 DSM 15936
NCBI: GCA_000425445.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.68	yes
125438	anaerobic	anaerobicⓘ	no	97.31	yes
125438	aerobic	aerobicⓘ	yes	86.05	no
125438	spore-forming	spore-formingⓘ	no	88.29	no
125438	thermophilic	thermophileⓘ	no	98.92	yes
125438	flagellated	motile2+ⓘ	no	93.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome sequencing and metabolic network reconstruction of a novel sulfur-oxidizing bacterium Acidithiobacillus Ameehan.	Wu P, Yuan Q, Cheng T, Han Y, Zhao W, Liao X, Wang L, Cai J, He Q, Guo Y, Zhang X, Lu F, Wang J, Ma H, Huang Z.	Front Microbiol	10.3389/fmicb.2023.1277847	2023
Transcriptome	Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space.	Helbert W, Poulet L, Drouillard S, Mathieu S, Loiodice M, Couturier M, Lombard V, Terrapon N, Turchetto J, Vincentelli R, Henrissat B.	Proc Natl Acad Sci U S A	10.1073/pnas.1815791116	2019
Metabolism	Metabolites Involved in Aerobic Degradation of the A and B Rings of Estrogen.	Wu K, Lee TH, Chen YL, Wang YS, Wang PH, Yu CP, Chu KH, Chiang YR.	Appl Environ Microbiol	10.1128/aem.02223-18	2019
Metabolism	Characterization of a Novel cis-3-Hydroxy-l-Proline Dehydratase and a trans-3-Hydroxy-l-Proline Dehydratase from Bacteria.	Watanabe S, Fukumori F, Miyazaki M, Tagami S, Watanabe Y.	J Bacteriol	10.1128/jb.00255-17	2017
Transcriptome	Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge.	Wei ST, Wu YW, Lee TH, Huang YS, Yang CY, Chen YL, Chiang YR.	mSystems	10.1128/msystems.00113-18	2018
Phylogeny	Flavobacterium movens sp. nov. and Flavobacterium mesophilum sp. nov., two novel bacteria isolated from rhizosphere soil of Litchi (Litchi chinensis Sonn.).	Dong Y, Wang X, Liu Y, Feng GD, Yao Q, Zhu H.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006908	2025
Phylogeny	Sphingosinicella humi sp. nov., isolated from arsenic-contaminated farmland soil and emended description of the genus Sphingosinicella.	Qiao Z, Cao M, Wang D, Liao S, Wang G.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003186	2019
Phylogeny	Povalibacter uvarum gen. nov., sp. nov., a polyvinyl-alcohol-degrading bacterium isolated from grapes.	Nogi Y, Yoshizumi M, Hamana K, Miyazaki M, Horikoshi K.	Int J Syst Evol Microbiol	10.1099/ijs.0.062620-0	2014
Metabolism	Denitratisoma oestradiolicum gen. nov., sp. nov., a 17beta-oestradiol-degrading, denitrifying betaproteobacterium.	Fahrbach M, Kuever J, Meinke R, Kampfer P, Hollender J.	Int J Syst Evol Microbiol	10.1099/ijs.0.63672-0	2006
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 )
#27716	IJSEM 1255 2005 ( DOI 10.1099/ijs.0.63484-0 , PubMed 15879265 )
#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
#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 .
#118896	Collection of Institut Pasteur ; Curators of the CIP; CIP 109214
#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 )

Rate our new design

Content

About us

Flavobacterium denitrificans (DSM 15936, ATCC BAA-842, CIP 109214)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000425445

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media