Name: Diaphorobacter nitroreducens NA10B
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2956

Type strain:

Species: Diaphorobacter nitroreducens

Strain Designation: NA10B

Culture col. no.: DSM 15985, CIP 107294, JCM 11421

Strain history: A. Hiraishi NA10B.

NCBI tax ID(s): 1236961 (strain), 164759 (species)

SI-ID 111712

CIP 107294, DSM 15985

Special Collections

Other strains from Diaphorobacter nitroreducens

Section

Diaphorobacter nitroreducens NA10B is a Gram-negative bacterium that was isolated from activated sludge.

Gram-negative
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	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Diaphorobacter*
	Species	**Diaphorobacter nitroreducens**
	Full Scientific Name (LPSN)	Diaphorobacter nitroreducens Khan and Hiraishi 2003

Synonym

Diaphorobacter polyhydroxybutyrativorans

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %97.468

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6221]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #6221]

Culture medium growth

[Ref.: #6221]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6221]

Culture medium composition

expand / minimize

[Ref.: #6221]

Culture medium

REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a)

[Ref.: #6221]

Culture medium growth

[Ref.: #6221]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6221]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #6221]			growth	28 °C
[Ref.: #67770]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]	Ability of spore formation	no Confidence in %91.069
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

[Ref.: #67770]

Observation

quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #6221]	23379	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	+

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

[Ref.: #6221]	Sample type/isolated from	activated sludge
[Ref.: #6221]	Country	Japan
[Ref.: #6221]	Country ISO 3 Code	JPN
[Ref.: #6221]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Activated sludge from sewage treatment plants
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	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 AB064317 (>99% sequence identity) for Diaphorobacter nitroreducens from Microbeatlas

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

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

[Ref.: #6221]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #6221]	Diaphorobacter nitroreducens gene for 16S rRNA, partial sequence, strain:NA10B	AB064317	1521	GenBank ENA	164759 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Diaphorobacter nitroreducens DSM 15985	GCA_003755025	contig	GenBank ENA	164759 tax ID
[Ref.: #66792]	Diaphorobacter nitroreducens JCM 11421	GCA_001310795	contig	GenBank ENA	1236961 tax ID	*
[Ref.: #66792]	Diaphorobacter nitroreducens JCM 11421	1236961.5	wgs	PATRIC	1236961 tax ID	*
[Ref.: #66792]	Diaphorobacter nitroreducens strain DSM 15985	164759.3	wgs	PATRIC	164759 tax ID	*
[Ref.: #66792]	Diaphorobacter nitroreducens JCM 11421	2728369657	draft	JGI IMG/M	1236961 tax ID	*
[Ref.: #66792]	Diaphorobacter nitroreducens DSM 15985	2786546147	draft	JGI IMG/M	164759 tax ID	*

[Ref.: #6221]	GC-content	65 mol%
[Ref.: #67770]	GC-content	65 mol%	high performance liquid chromatography (HPLC)

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: Diaphorobacter nitroreducens JCM 11421 PATRIC: 1236961.5
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Diaphorobacter nitroreducens JCM 11421 PATRIC: 1236961.5
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.468	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	94.451	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	91.069	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	78.787	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.815	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	71.079	no

Availability in culture collections External links

[Ref.: #6221]

Culture collection no.

DSM 15985, CIP 107294, JCM 11421

[Ref.: #72478]

SI-ID 111712

Literature:

Only first 10 entries are displayed. Click here to see all.

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	*
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	*
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 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	*
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	*

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 .

#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 )

#72478

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-ID111712.1 )

* These data were automatically processed and therefore are not curated

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Diaphorobacter nitroreducens JCM 11421

Diaphorobacter nitroreducens JCM 11421

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