Strain identifier

BacDive ID: 10770

Type strain: Yes

Species: Nocardia vinacea

Strain Designation: MK703-102F1

Strain history: CIP <- 2002, JCM <- 2000, M. Hamada: strain MK703-102F1

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 11947

BacDive-ID: 10770

DSM-Number: 44638

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, human pathogen

description: Nocardia vinacea MK703-102F1 is a facultative anaerobe, spore-forming, mesophilic human pathogen that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1206742strain
96468species

strain history

@refhistory
11947<- T. Kudo, JCM <- M. Hamada; MK703-102F1
67770M. Hamada MK703-102F1 (IMC A-0211).
123843CIP <- 2002, JCM <- 2000, M. Hamada: strain MK703-102F1

doi: 10.13145/bacdive10770.20230509.8.1

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 vinacea
  • full scientific name: Nocardia vinacea Kinoshita et al. 2002

@ref: 11947

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia vinacea

full scientific name: Nocardia vinacea Kinoshita et al. 2002

strain designation: MK703-102F1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no96.742
69480100positive
123843nopositiverod-shaped

colony morphology

@refcolony colormedium usedhemolysis ability
69359Beige (1001)ISP 2
69359Beige (1001)ISP 6
69359Maize yellow (1006)ISP 4
69359Ochre brown (8001)ISP 7
69359Pastel yellow (1034)ISP 3
69359Sun yellow (1037)suter with tyrosine
69359Sun yellow (1037)suter without tyrosine
69359Terra brown (8028)ISP 5
1238431

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69359yesAerial myceliumCream (9001)ISP 2
69359noAerial myceliumISP 3
69359noAerial myceliumISP 4
69359yesAerial myceliumSignal white (9003)ISP 5
69359noAerial myceliumISP 6
69359yesAerial myceliumTraffic white (9016)ISP 7
69359yesAerial myceliumCream (9001)suter with tyrosine
69359yesAerial myceliumCream (9001)suter without tyrosine

pigmentation

@refproductionnamecolor
69359yesMelanin
69359yessoluble pigmentBeige (1001), brown beige (1011)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11947GYM 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
33757MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
123843CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11947positivegrowth28mesophilic
33757positivegrowth30mesophilic
67770positivegrowth28mesophilic
123843positivegrowth25-41
123843nogrowth10psychrophilic
123843nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123843
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481yes100
69480no99.456

halophily

@refsaltgrowthtested relationconcentration
69359NaClpositivegrowth0-2.5 %
123843NaClpositivegrowth0 %
123843NaClnogrowth2 %
123843NaClnogrowth4 %
123843NaClnogrowth6 %
123843NaClnogrowth8 %
123843NaClnogrowth10 %

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
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
68371turanose-builds acid from32528
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
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
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-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68369malate+assimilation25115
68369decanoate-assimilation27689
68369N-acetylglucosamine+assimilation59640
68369D-mannitol+assimilation16899
68369L-arabinose+assimilation30849
68369D-glucose+assimilation17634
68369gelatin-hydrolysis5291
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
69359arabinose+growth22599
69359cellulose-growth62968
69359fructose+/-growth28757
69359glucose+growth17234
69359inositol+/-growth17268
69359mannose+/-growth37684
69359raffinose-growth16634
69359rhamnose-growth26546
69359sucrose-growth17992
69359xylose-growth18222
123843esculin+hydrolysis4853
123843hippurate-hydrolysis606565
123843nitrate+reduction17632
123843nitrite-reduction16301
123843nitrate+respiration17632
68379nitrate-reduction17632
68379esculin-hydrolysis4853
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

antibiotic resistance

  • @ref: 123843
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6777066279tubelactomicin Ayes
12384335581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12384315688acetoin-
12384317234glucose-

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
68369gelatinase-
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123843oxidase-
123843beta-galactosidase+3.2.1.23
123843alcohol dehydrogenase-1.1.1.1
123843gelatinase-
123843amylase-
123843caseinase-3.4.21.50
123843catalase+1.11.1.6
123843tween esterase-
123843gamma-glutamyltransferase-2.3.2.2
123843lecithinase-
123843lipase-
123843lysine decarboxylase+4.1.1.18
123843ornithine decarboxylase-4.1.1.17
123843phenylalanine ammonia-lyase-4.3.1.24
123843tryptophan deaminase-
123843urease+3.5.1.5
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
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 NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69359------+------------

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
11947-++/-+/-------+/-----++/----
69359+/-+/-++/-+/-----++/----++---
123843--+--+----+----++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
11947+/-----+/---+++/-+++/-+/--+/-++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123843----------------------------------------+/--------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123843-+----------------++-----------+-----------+++----++-+--+--++-+--++-------------+-----+-+-++----+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11947soilSuwa-shi, Nagano PrefectureJapanJPNAsia
67770SoilSuwa-shi, Nagano Pref.JapanJPNAsia
123843Environment, SoilSuwashi, NaganoJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6347.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_1916;98_2357;99_6347&stattab=map
  • Last taxonomy: Nocardia vinacea
  • 16S sequence: GQ853073
  • Sequence Identity:
  • Total samples: 52
  • soil counts: 43
  • aquatic counts: 7
  • animal counts: 1
  • plant counts: 1

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
11947yes, in single cases1Risk group (German classification)
1238432Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia vinacea strain DSM 44638 16S ribosomal RNA gene, partial sequenceJN041530462ena96468
20218Nocardia vinacea gene for 16S ribosomal RNAAB0243121476ena96468
20218Nocardia vinacea strain JCM 10988 16S ribosomal RNA gene, partial sequenceAY756567606ena96468
20218Nocardia vinacea strain JCM 10988 16S ribosomal RNA gene, partial sequenceDQ6599191419ena96468
20218Nocardia vinacea strain W7850 16S ribosomal RNA gene, partial sequenceGQ8530731439ena96468

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia vinacea NBRC 164971206742.4wgspatric1206742
66792Nocardia vinacea NBRC 164972551306192draftimg1206742
67770Nocardia vinacea NBRC 16497GCA_000308835contigncbi1206742

GC content

@refGC-contentmethod
6777065.5genome sequence analysis
6777065high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.636no
gram-positiveyes84.192no
anaerobicno99.175no
aerobicyes89.209no
halophileno94.056no
spore-formingyes84.325no
glucose-utilyes90.131no
flagellatedno97.981no
thermophileno99.299yes
glucose-fermentno90.464yes

External links

@ref: 11947

culture collection no.: DSM 44638, CIP 107372, FERM P-16580, IFO 16497, JCM 10988, NBRC 16497, IFM 10175

straininfo link

  • @ref: 80038
  • straininfo: 88659

literature

  • topic: Pathogenicity
  • Pubmed-ID: 35450515
  • title: Identification of a novel drug-resistant community-acquired Nocardia spp. in a patient with bronchiectasis.
  • authors: Li Z, Li Y, Li S, Li Z, Mai Y, Cheng J, Su D, Zhan Y, Zhong N, Ye F
  • journal: Emerg Microbes Infect
  • DOI: 10.1080/22221751.2022.2069514
  • year: 2022
  • mesh: Animals, *Bronchiectasis/epidemiology, Humans, Immunocompromised Host, Mice, *Nocardia/genetics, *Nocardia Infections/drug therapy/epidemiology, *Pneumonia

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11947Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44638)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44638
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
33757Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4800
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
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69359Wink, J.https://cdn.dsmz.de/wink/DSM%2044638.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
80038Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88659.1StrainInfo: A central database for resolving microbial strain identifiers
123843Curators of the CIPCollection of Institut Pasteur (CIP 107372)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107372