Diaphorobacter nitroreducens (DSM 15985, CIP 107294, JCM 11421)

Name: Diaphorobacter nitroreducens (DSM 15985, CIP 107294, JCM 11421)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2956

Type strain

Strain Designation NA10B

Culture col. no. DSM 15985 CIP 107294 JCM 11421 NA10B

NCBI tax ID(s) 1236961 164759

Special Collections DSMZ JCM CIP

History <- A. Hiraishi; NA10B A. Hiraishi NA10B.

Links

Diaphorobacter nitroreducens NA10B is a mesophilic prokaryote that was isolated from activated sludge.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 111712

JCM 11421,CIP 107294,DSM 15985

@ref 20215

Last LPSN update 2026-02-09 11:18:23

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Diaphorobacter

Species Diaphorobacter nitroreducens

Full scientific name Diaphorobacter nitroreducens Khan and Hiraishi 2003

Synonyms (1)

Diaphorobacter polyhydroxybutyrativorans

BacDive ID	Other strains from **Diaphorobacter nitroreducens** (1)	Type strain
130259	D. nitroreducens SL-205, DSM 29460, ACCC 19739, JCM 30411 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.468
125439	negative	98.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6221	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
6221	REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a)		Medium recipe at MediaDive	Name: REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a) Composition: Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6221	positive	growth	28	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125438		91.069
125439		98.6

Observation

67770

Observationquinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
6221	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Activated sludge

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
6221	activated sludge	Japan	JPN	Asia
67770	Activated sludge from sewage treatment plants	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB064317 (>99% sequence identity) for Diaphorobacter nitroreducens from Microbeatlas

Aquatic Samples	6609
Soil Samples	4505
Animal Samples	8073
Plant Samples	2013
Total Samples	21200

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6221	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM375502v1 assembly for Diaphorobacter nitroreducens DSM 15985	contig	GCA_003755025	164759.3	2786546147	164759	76.56
66792	ASM131079v1 assembly for Diaphorobacter nitroreducens JCM 11421	contig	GCA_001310795	1236961.5	2728369657	1236961

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6221	Diaphorobacter nitroreducens gene for 16S rRNA, partial sequence, strain:NA10B	AB064317	1521		164759

GC content

@ref	GC-content (mol%)	Method
6221	65
67770	65	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Diaphorobacter nitroreducens JCM 11421
NCBI: GCA_001310795

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	84.60	no
125439	gram_stain	BacteriaNetⓘ	negative	98.50	no
125439	motility	BacteriaNetⓘ	yes	81.10	no
125439	spore_formation	BacteriaNetⓘ	no	98.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Diaphorobacter nitroreducens JCM 11421
PATRIC: 1236961.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.47	no
125438	anaerobic	anaerobicⓘ	no	94.45	no
125438	spore-forming	spore-formingⓘ	no	91.07	no
125438	aerobic	aerobicⓘ	yes	78.79	no
125438	thermophilic	thermophileⓘ	no	94.82	yes
125438	flagellated	motile2+ⓘ	yes	71.08	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Diaphorobacter polyhydroxybutyrativorans Qiu et al. 2015 is a later heterotypic synonym of Diaphorobacter nitroreducens Khan and Hiraishi 2003.	Liu Y, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003582	2019
Metabolism	Bacterial community dynamics in a biodenitrification reactor packed with polylactic acid/poly (3-hydroxybutyrate-co-3-hydroxyvalerate) blend as the carbon source and biofilm carrier.	Qiu T, Xu Y, Gao M, Han M, Wang X	J Biosci Bioeng	10.1016/j.jbiosc.2016.12.007	2017
Phylogeny	Diaphorobacter nitroreducens gen nov, sp nov, a poly(3-hydroxybutyrate)-degrading denitrifying bacterium isolated from activated sludge.	Khan ST, Hiraishi A	J Gen Appl Microbiol	10.2323/jgam.48.299	2002
Phylogeny	Pulveribacter suum gen. nov., sp. nov., isolated from a pig farm dust collector.	Heo J, Cho HY, Heo I, Hong SB, Kim JS, Kwon SW, Kim SJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003082	2019
Phylogeny	Diaphorobacter polyhydroxybutyrativorans sp. nov., a novel poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-degrading bacterium isolated from biofilms.	Qiu T, Zuo Z, Gao J, Gao M, Han M, Sun L, Zhang L, Wang X	Int J Syst Evol Microbiol	10.1099/ijs.0.000353	2015
Phylogeny	Diaphorobacter ruginosibacter sp. nov., isolated from soybean root nodule, and emended description of the genus Diaphorobacter.	Wei XL, Han MS, Xia CC, Ding SL, Xu L, Lin YB, Wang L, Wei GH	Arch Microbiol	10.1007/s00203-015-1102-7	2015
Phylogeny	Diaphorobacter aerolatus sp. nov., isolated from air, and emended description of the genus Diaphorobacter.	Kim SJ, Moon JY, Ahn JH, Weon HY, Hong SB, Seok SJ, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.051060-0	2013
Phylogeny	Diaphorobacter oryzae sp. nov., isolated from a thiosulfate-oxidizing enrichment culture.	Pham VH, Park SJ, Roh Y, Roh DH, Rhee SK	Int J Syst Evol Microbiol	10.1099/ijs.0.001669-0	2009

References

#6221	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15985
#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 )
#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;
#68369	Automatically annotated from API 20NE .
#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 .
#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 )

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Diaphorobacter nitroreducens (DSM 15985, CIP 107294, JCM 11421)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003755025

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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