Strain identifier

BacDive ID: 10722

Type strain: Yes

Species: Nocardia mexicana

Strain history: CIP <- 2004, P. Boiron, Fac. Pharmacie ISPB, Lyon, France: strain OFN 785-81

NCBI tax ID(s): 1210089 (strain), 279262 (species)

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General

@ref: 12205

BacDive-ID: 10722

DSM-Number: 44952

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic

description: Nocardia mexicana DSM 44952 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from pus samples of Mexican patients.

NCBI tax id

NCBI tax idMatching level
1210089strain
279262species

strain history

@refhistory
12205<- V. Rodríguez-Nava
67770IFM 10801 <-- DSM 44952 <-- V. Rodríguez-Nava OFN 785.81.
120928CIP <- 2004, P. Boiron, Fac. Pharmacie ISPB, Lyon, France: strain OFN 785-81

doi: 10.13145/bacdive10722.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Nocardiaceae
  • genus: Nocardia
  • species: Nocardia mexicana
  • full scientific name: Nocardia mexicana Rodríguez-Nava et al. 2006

@ref: 12205

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia mexicana

full scientific name: Nocardia mexicana Rodríguez-Nava et al. 2006

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no97.442
69480100positive
120928nopositivefilament-shaped

colony morphology

@refcolony colormedium used
69367ColourlessISP 6
69367Colourlesssuter with tyrosine
69367Colourlesssuter without tyrosine
69367ColourlessISP 3
69367ColourlessISP 4
69367Olive brown (8008)ISP 5
69367Sand yellow (1002)ISP 2
69367Terra brown (8028)ISP 7
120928

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69367yesAerial myceliumCream (9001)ISP 2
69367noAerial myceliumISP 3
69367noAerial myceliumISP 4
69367yesAerial myceliumCream (9001)ISP 5
69367noAerial myceliumISP 6
69367yesAerial myceliumLight ivory (1015)ISP 7
69367noAerial myceliumsuter with tyrosine
69367noAerial myceliumsuter without tyrosine

pigmentation

@refproductionnamecolor
69367noMelanin
69367yessoluble pigmentBrown beige(1011)

multimedia

@refmultimedia contentcaptionintellectual property rights
12205https://www.dsmz.de/microorganisms/photos/DSM_44952.jpgMedium 65 28°C© Leibniz-Institut DSMZ
69367DSM_44952_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69367DSM_44952_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12205GYM 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
37423MEDIUM 129 - for Pseudonocardia, Nocardia, Skermania and Streptomyces seoulensis, Streptomyces stramineusyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (10.000g);Yeast extract (1.000 g);Beef extract (1.000 g);Casamino acids (2.000 g)
120928CIP Medium 129yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=129

culture temp

@refgrowthtypetemperaturerange
12205positivegrowth28mesophilic
37423positivegrowth37mesophilic
67770positivegrowth28mesophilic
120928positivegrowth25-37mesophilic
120928nogrowth10psychrophilic
120928nogrowth41thermophilic
120928nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
12205aerobe
120928obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 99

halophily

@refsaltgrowthtested relationconcentration
69367NaClpositivegrowth0-5 %
120928NaClpositivegrowth0-4 %
120928NaClnogrowth6 %
120928NaClnogrowth8 %
120928NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4, ω-cycl)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6936722599arabinose-growth
6936762968cellulose-growth
6936728757fructose+growth
6936717234glucose+growth
6936717268inositol+growth
6936737684mannose+growth
6936716634raffinose-growth
6936726546rhamnose+growth
6936717992sucrose-growth
6936718222xylose-growth
12092816947citrate-carbon source
1209284853esculin+hydrolysis
120928606565hippurate-hydrolysis
12092817632nitrate-reduction
12092816301nitrite-reduction
12092817632nitrate-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

metabolite production

  • @ref: 120928
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12092815688acetoin-
12092817234glucose-

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
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
120928oxidase-
120928beta-galactosidase+3.2.1.23
120928alcohol dehydrogenase-1.1.1.1
120928gelatinase-
120928amylase-
120928DNase-
120928caseinase-3.4.21.50
120928catalase+1.11.1.6
120928tween esterase-
120928gamma-glutamyltransferase+2.3.2.2
120928lecithinase-
120928lipase-
120928lysine decarboxylase-4.1.1.18
120928ornithine decarboxylase-4.1.1.17
120928phenylalanine ammonia-lyase-4.3.1.24
120928protease-
120928tryptophan deaminase-
120928urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
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-glucuronidase-3.2.1.31
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69367+--+---------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
69367+++/--+----++-+/--+/-+---
120928+++-+----++-+-++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120928+--+--------------+------------+-----------------+-------------------------+----+-------+-+--+----+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
12205pus samples of Mexican patientsMexicoMEXNorth America
67770Pus samples of Mexican patients with mycetomasMexicoMEXNorth America
120928Human, MycetomasMexicoMEXNorth America1960

isolation source categories

Cat1Cat2
#Infection#Patient
#Host Body Product#Fluids

taxonmaps

  • @ref: 69479
  • File name: preview.99_6079.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_3563;98_4510;99_6079&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: JF797310
  • Sequence Identity:
  • Total samples: 86
  • soil counts: 60
  • aquatic counts: 4
  • animal counts: 15
  • plant counts: 7

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
122052Risk group (German classification)
1209282Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia mexicana partial 16S rRNA gene, type strain DSM44952TFR7337231504ena279262
20218Nocardia mexicana 16S ribosomal RNA gene, partial sequenceGQ3761781439ena279262
20218Nocardia mexicana strain DSM 44952 16S ribosomal RNA gene, partial sequenceJF7973101412ena279262
12205Nocardia mexicana strain CIP 108295 isolate VNS29 16S ribosomal RNA gene, partial sequenceAY903610606ena279262
67770Nocardia mexicana strain OFN 785.81 16S ribosomal RNA gene, partial sequenceAY5555771329ena279262

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia mexicana NBRC 1082441210089.4wgspatric1210089
66792Nocardia mexicana strain DSM 44952279262.5wgspatric279262
66792Nocardia mexicana DSM 449522770939516draftimg279262
66792Nocardia mexicana NBRC 1082442698536635draftimg1210089
67770Nocardia mexicana NBRC 108244GCA_001613165contigncbi1210089
67770Nocardia mexicana DSM 44952GCA_003350525scaffoldncbi279262

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
motileno91.439no
gram-positiveyes89.103no
anaerobicno99.175yes
aerobicyes87.071yes
halophileno88.374no
spore-formingyes80.682no
thermophileno98.747yes
glucose-utilyes89.899yes
flagellatedno98.037no
glucose-fermentno89.495yes

External links

@ref: 12205

culture collection no.: DSM 44952, CIP 108295, JCM 14590, IFM 10801, NBRC 108244, OFN 785-81

straininfo link

  • @ref: 79991
  • straininfo: 289771

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21742817Nocardia goodfellowii sp. nov. and Nocardia thraciensis sp. nov., isolated from soil.Sazak A, Sahin N, Camas MInt J Syst Evol Microbiol10.1099/ijs.0.031559-02011DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Nocardia/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny25939264Isolation of Nocardia mexicana from focal proliferative tenosynovitis and arthritis in a steer.Owen H, Buckle K, Olm J, Leitner M, Pandey S, Gaughan JB, Sullivan ML, Lees AM, Gibson JSAust Vet J10.1111/avj.123082015Animals, Anti-Bacterial Agents/pharmacology, Arthritis, Infectious/etiology/microbiology/*veterinary, Australia/epidemiology, Cattle, Cephalosporins/pharmacology, Male, Microbial Sensitivity Tests/veterinary, Nocardia/drug effects/genetics/*isolation & purification, Nocardia Infections/complications/epidemiology/microbiology/*veterinary, RNA, Ribosomal, 16S/genetics, Stifle/microbiology, Tenosynovitis/etiology/microbiology/*veterinary, Trimethoprim, Sulfamethoxazole Drug Combination/pharmacologyEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12205Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44952)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44952
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
37423Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5901
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69367Wink, J.https://cdn.dsmz.de/wink/DSM%2044952.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
79991Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289771.1StrainInfo: A central database for resolving microbial strain identifiers
120928Curators of the CIPCollection of Institut Pasteur (CIP 108295)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108295