Strain identifier

BacDive ID: 2956

Type strain: Yes

Species: Diaphorobacter nitroreducens

Strain Designation: NA10B

Strain history: A. Hiraishi NA10B.

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

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General

@ref: 6221

BacDive-ID: 2956

DSM-Number: 15985

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative

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

NCBI tax id

NCBI tax idMatching level
164759species
1236961strain

strain history

@refhistory
6221<- A. Hiraishi; NA10B
67770A. Hiraishi NA10B.

doi: 10.13145/bacdive2956.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • 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

    • @ref: 20215
    • synonym: Diaphorobacter polyhydroxybutyrativorans

@ref: 6221

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Diaphorobacter

species: Diaphorobacter nitroreducens

full scientific name: Diaphorobacter nitroreducens Khan and Hiraishi 2003

strain designation: NA10B

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 97.468

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6221TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
6221REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a)yeshttps://mediadive.dsmz.de/medium/220aName: 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

@refgrowthtypetemperature
6221positivegrowth28
67770positivegrowth30

Physiology and metabolism

spore formation

@refspore formationconfidence
69480no91.069
69481no100

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6221+-------------+--+--+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6221activated sludgeJapanJPNAsia
67770Activated sludge from sewage treatment plantsJapanJPNAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_1320.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_491;97_892;98_1045;99_1320&stattab=map
  • Last taxonomy: Diaphorobacter nitroreducens
  • 16S sequence: AB064317
  • Sequence Identity:
  • Total samples: 21200
  • soil counts: 4505
  • aquatic counts: 6609
  • animal counts: 8073
  • plant counts: 2013

Safety information

risk assessment

  • @ref: 6221
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6221
  • description: Diaphorobacter nitroreducens gene for 16S rRNA, partial sequence, strain:NA10B
  • accession: AB064317
  • length: 1521
  • database: nuccore
  • NCBI tax ID: 164759

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Diaphorobacter nitroreducens JCM 11421GCA_001310795contigncbi1236961
66792Diaphorobacter nitroreducens JCM 114211236961.5wgspatric1236961
66792Diaphorobacter nitroreducens strain DSM 15985164759.3wgspatric164759
66792Diaphorobacter nitroreducens JCM 114212728369657draftimg1236961
66792Diaphorobacter nitroreducens DSM 159852786546147draftimg164759
67770Diaphorobacter nitroreducens DSM 15985GCA_003755025contigncbi164759

GC content

@refGC-contentmethod
622165
6777065high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.468no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.451no
69480spore-formingspore-formingAbility to form endo- or exosporesno91.069no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes78.787no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.815yes
69480flagellatedmotile2+Ability to perform flagellated movementyes71.079no

External links

@ref: 6221

culture collection no.: DSM 15985, CIP 107294, JCM 11421

straininfo link

  • @ref: 72478
  • straininfo: 111712

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12682868Diaphorobacter nitroreducens gen nov, sp nov, a poly(3-hydroxybutyrate)-degrading denitrifying bacterium isolated from activated sludge.Khan ST, Hiraishi AJ Gen Appl Microbiol10.2323/jgam.48.2992002Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/*genetics/isolation & purification/physiology, DNA, Ribosomal/analysis, Hydroxybutyrates/*metabolism, Molecular Sequence Data, Nitrites/*metabolism, Nucleic Acid Hybridization, Phenotype, Polyesters/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiologyMetabolism
Phylogeny19196757Diaphorobacter oryzae sp. nov., isolated from a thiosulfate-oxidizing enrichment culture.Pham VH, Park SJ, Roh Y, Roh DH, Rhee SKInt J Syst Evol Microbiol10.1099/ijs.0.001669-02009Bacteriological Techniques, Comamonadaceae/chemistry/*classification/genetics/metabolism, Culture Media, Fatty Acids, Molecular Sequence Data, Oxidation-Reduction, Phenotype, RNA, Ribosomal, 16S/genetics, Species Specificity, Thiosulfates/*metabolismMetabolism
Phylogeny24105945Diaphorobacter 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 SWInt J Syst Evol Microbiol10.1099/ijs.0.051060-02013*Air Microbiology, Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny25763990Diaphorobacter 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 GHArch Microbiol10.1007/s00203-015-1102-72015Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Phylogeny, Quinones, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Sodium Chloride, Soybeans/*microbiologyTranscriptome
Phylogeny26012582Diaphorobacter 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 XInt J Syst Evol Microbiol10.1099/ijs.0.0003532015Animals, Bacterial Typing Techniques, Base Composition, Beijing, *Biofilms, Bioreactors/*microbiology, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Manure, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Polyesters/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/microbiology, Swine, Ubiquinone/chemistryGenetics
Metabolism28082241Bacterial 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 XJ Biosci Bioeng10.1016/j.jbiosc.2016.12.00720173-Hydroxybutyric Acid/*metabolism/pharmacology, Betaproteobacteria/classification/genetics/isolation & purification/*metabolism, Biodegradation, Environmental, *Biofilms/drug effects, Bioreactors/*microbiology, Carbon/*metabolism/pharmacology, Comamonadaceae/classification/genetics/isolation & purification/metabolism, *Denitrification, Nitrates/isolation & purification/metabolism, Nitrogen/isolation & purification/metabolism, Pentanoic Acids/*metabolism/pharmacology, Polyesters/*metabolism/pharmacology, Polymers/*metabolism/pharmacology, RNA, Ribosomal, 16S/genetics, Sewage/microbiology, Waste Water/chemistryPhylogeny
Phylogeny31046896Pulveribacter 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 SJInt J Syst Evol Microbiol10.1099/ijsem.0.0030822019Animals, Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/isolation & purification, DNA, Bacterial/genetics, *Dust, *Farms, Fatty Acids/chemistry, Genes, Bacterial, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Swine, Ubiquinone/chemistryTranscriptome
Phylogeny31282854Diaphorobacter polyhydroxybutyrativorans Qiu et al. 2015 is a later heterotypic synonym of Diaphorobacter nitroreducens Khan and Hiraishi 2003.Liu Y, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0035822019Animals, Bacterial Typing Techniques, Base Composition, Bioreactors/microbiology, Comamonadaceae/*classification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, SwineTranscriptome

Reference

@idauthorscataloguedoi/urltitle
6221Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15985)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15985
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
72478Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID111712.1StrainInfo: A central database for resolving microbial strain identifiers