Strain identifier

BacDive ID: 10604

Type strain: Yes

Species: Gordonia namibiensis

Strain Designation: NAM-BN063A

Strain history: CIP <- 2002, NCIMB <- M. Goodfellow, Newcastle Univ., Newcastle, UK: strain NAM-BN063A

NCBI tax ID(s): 1208314 (strain), 168480 (species)

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General

@ref: 11764

BacDive-ID: 10604

DSM-Number: 44568

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

description: Gordonia namibiensis NAM-BN063A is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
168480species
1208314strain

strain history

@refhistory
11764<- M. Goodfellow, Univ. Newcastle; NAM-BN063A
67770NCIMB 13800 <-- M. Goodfellow NAM-BN063A.
121228CIP <- 2002, NCIMB <- M. Goodfellow, Newcastle Univ., Newcastle, UK: strain NAM-BN063A

doi: 10.13145/bacdive10604.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Gordoniaceae
  • genus: Gordonia
  • species: Gordonia namibiensis
  • full scientific name: Gordonia namibiensis Brandão et al. 2002

@ref: 11764

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia namibiensis

full scientific name: Gordonia namibiensis Brandão et al. 2002

strain designation: NAM-BN063A

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
121228positiverod-shapedno

colony morphology

  • @ref: 121228

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11764TRYPTICASE 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
33147MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121228CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
11764positivegrowth28mesophilic
33147positivegrowth30mesophilic
67770positivegrowth28mesophilic
121228positivegrowth25-45
121228nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121228
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no98
69480no99.535

halophily

  • @ref: 121228
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12122816947citrate-carbon source
1212284853esculin-hydrolysis
121228606565hippurate-hydrolysis
12122817632nitrate-reduction
12122816301nitrite-reduction
12122817632nitrate-respiration
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 121228
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 121228
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12122815688acetoin-
12122817234glucose-

enzymes

@refvalueactivityec
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrazinamidase-3.5.1.B15
121228oxidase-
121228beta-galactosidase-3.2.1.23
121228alcohol dehydrogenase-1.1.1.1
121228gelatinase-
121228amylase-
121228DNase-
121228caseinase-3.4.21.50
121228catalase+1.11.1.6
121228tween esterase+
121228gamma-glutamyltransferase+2.3.2.2
121228lecithinase-
121228lipase-
121228lysine decarboxylase-4.1.1.18
121228ornithine decarboxylase-4.1.1.17
121228phenylalanine ammonia-lyase-4.3.1.24
121228protease-
121228tryptophan deaminase-
121228urease+3.5.1.5
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382alpha-chymotrypsin-3.4.21.1
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYG
11764--+/-+--+-------------

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
11764-+/--+/--+----+/-----+----
121228-+++-++++-++---++---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121228-+-+---+------------------+------+--+------------+---+------+------+-----------+++--+---+-------+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11764soilKalahariNamibiaNAMAfrica
67770Kalahari soilWaterberg area of Central NamibiaNamibiaNAMAfrica
121228Environment, Namibian soilKalahariNamibiaNAMAfrica1997

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5412.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_90;98_746;99_5412&stattab=map
  • Last taxonomy: Gordonia
  • 16S sequence: AF380930
  • Sequence Identity:
  • Total samples: 196
  • soil counts: 28
  • aquatic counts: 44
  • animal counts: 117
  • plant counts: 7

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
117641Risk group (German classification)
1212281Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11764
  • description: Gordonia namibiensis NAM-BN063A 16S ribosomal RNA gene, partial sequence
  • accession: AF380930
  • length: 1484
  • database: ena
  • NCBI tax ID: 1208314

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia namibiensis NBRC 1082291208314.3wgspatric1208314
66792Gordonia namibiensis NBRC 1082292523231041draftimg1208314
67770Gordonia namibiensis NBRC 108229GCA_000298235contigncbi1208314

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileno94.253no
gram-positiveyes87.346no
anaerobicno99.43no
aerobicyes91.396no
halophileno81.591no
spore-formingno82.134no
glucose-utilyes89.259no
flagellatedno98.762no
glucose-fermentno90.641no
thermophileno98.743yes

External links

@ref: 11764

culture collection no.: DSM 44568, NCIMB 13800, JCM 12074, BCRC 16392, CCUG 47264, CIP 107614, IFM 10356, KCTC 9952, NBRC 108229

straininfo link

  • @ref: 79878
  • straininfo: 43769

literature

  • topic: Phylogeny
  • Pubmed-ID: 11876358
  • title: Gordonia namibiensis sp. nov., a novel nitrile metabolising actinomycete recovered from an African sand.
  • authors: Brandao PF, Maldonado LA, Ward AC, Bull AT, Goodfellow M
  • journal: Syst Appl Microbiol
  • DOI: 10.1078/0723-2020-00074
  • year: 2001
  • mesh: Actinomycetales/*classification/genetics/metabolism, Base Sequence, DNA, Bacterial/chemistry/genetics, Molecular Sequence Data, Namibia, Nitriles/*metabolism, Phenotype, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
11764Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44568)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44568
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
33147Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5069
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
79878Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43769.1StrainInfo: A central database for resolving microbial strain identifiers
121228Curators of the CIPCollection of Institut Pasteur (CIP 107614)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107614