Strain identifier

BacDive ID: 11111

Type strain: Yes

Species: Nocardioides pyridinolyticus

Strain Designation: OS4

Strain history: CIP <- 2000, JCM <- KCTC <- S. -K. Rhee: strain OS4

NCBI tax ID(s): 1305854 (strain), 109465 (species)

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General

@ref: 5981

BacDive-ID: 11111

DSM-Number: 15530

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, motile, rod-shaped

description: Nocardioides pyridinolyticus OS4 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from oxic zone of an oil shale column.

NCBI tax id

NCBI tax idMatching level
109465species
1305854strain

strain history

@refhistory
5981<- JCM <- KCTC <- S.-K. Rhee; OS4
67770KCTC 0074BP <-- S.-K. Rhee OS4.
122090CIP <- 2000, JCM <- KCTC <- S. -K. Rhee: strain OS4

doi: 10.13145/bacdive11111.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides pyridinolyticus
  • full scientific name: Nocardioides pyridinolyticus Yoon et al. 1997

@ref: 5981

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides pyridinolyticus

full scientific name: Nocardioides pyridinolyticus Yoon et al. 1997

strain designation: OS4

type strain: yes

Morphology

cell morphology

  • @ref: 122090
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 122090

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5981GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
39582MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
122090CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
5981positivegrowth28mesophilic
39582positivegrowth37mesophilic
67770positivegrowth35mesophilic
122090positivegrowth25-37mesophilic
122090nogrowth10psychrophilic
122090nogrowth41thermophilic
122090nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122090
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
122090NaClpositivegrowth2-6 %
122090NaClnogrowth0 %
122090NaClnogrowth8 %
122090NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4), MK-7(H4), MK-8(H2)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
122090esculin+hydrolysis4853
122090hippurate-hydrolysis606565
122090nitrate+reduction17632
122090nitrite-reduction16301

antibiotic resistance

  • @ref: 122090
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122090
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12209015688acetoin-
12209017234glucose-

enzymes

@refvalueactivityec
122090oxidase-
122090beta-galactosidase+3.2.1.23
122090alcohol dehydrogenase-1.1.1.1
122090gelatinase+
122090amylase+
122090DNase+
122090caseinase+3.4.21.50
122090catalase+1.11.1.6
122090tween esterase-
122090gamma-glutamyltransferase+2.3.2.2
122090lysine decarboxylase-4.1.1.18
122090ornithine decarboxylase-4.1.1.17
122090phenylalanine ammonia-lyase-4.3.1.24
122090tryptophan deaminase-
122090urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122090-+++-++-+-++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122090----+/-+/-----+/-+/-+/--+/----------+/------+/---------+/----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122090++-+---+-++-+--+---+-+-+-+------+--+-----------------------+----------+----+------------+-------++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5981oxic zone of an oil shale columnRepublic of KoreaKORAsia
67770Oxic zone of an oil shale column
122090Oxic zone of an oil shale column

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Oil reservoir
#Environmental#Terrestrial#Geologic

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59811Risk group (German classification)
1220901Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5981
  • description: Nocardioides OS4 16S rRNA
  • accession: U61298
  • length: 1482
  • database: ena
  • NCBI tax ID: 1305854

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides pyridinolyticus JCM 10369GCA_001313985contigncbi1305854
66792Nocardioides pyridinolyticus JCM 103691305854.4wgspatric1305854
66792Nocardioides pyridinolyticus JCM 103692734481967draftimg1305854

GC content

@refGC-contentmethod
598172.5
6777072.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno62.546no
gram-positiveyes84.668no
anaerobicno97.979no
halophileno95.208no
spore-formingno93.99no
thermophileno96.817no
glucose-utilyes92.25no
aerobicyes93.049no
flagellatedno96.867no
glucose-fermentno89.904no

External links

@ref: 5981

culture collection no.: DSM 15530, CIP 106800, JCM 10369, KCTC 0074BP

straininfo link

  • @ref: 80360
  • straininfo: 63135

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9336889Nocardioides pyridinolyticus sp. nov., a pyridine-degrading bacterium isolated from the oxic zone of an oil shale column.Yoon JH, Rhee SK, Lee JS, Park YH, Lee STInt J Syst Bacteriol10.1099/00207713-47-4-9331997Base Composition, Cell Wall/physiology, DNA, Bacterial/*analysis, Fatty Acids/analysis, Galactose/analysis, Genes, Bacterial/genetics, Molecular Sequence Data, *Phylogeny, Propionibacteriaceae/chemistry/*classification/*genetics, Pyridines/*metabolism, RNA, Bacterial/*analysis, RNA, Ribosomal, 16S/*analysis, Ribose/analysisGenetics
Phylogeny18676470Nocardioides fonticola sp. nov., a novel actinomycete isolated from spring water.Chou JH, Cho NT, Arun AB, Young CC, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.65810-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, TaiwanGenetics
Phylogeny27381405Nocardioides intraradicalis sp. nov., isolated from the roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu.Huang MJ, Huang HQ, Salam N, Xiao M, Duan YQ, Kim CJ, Li QQ, Chen W, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0012742016Actinomycetales/*classification/genetics/isolation & purification, Base Composition, Caryophyllaceae/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
5981Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15530)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15530
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
39582Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18970
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/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
80360Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID63135.1StrainInfo: A central database for resolving microbial strain identifiers
122090Curators of the CIPCollection of Institut Pasteur (CIP 106800)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106800