Strain identifier

BacDive ID: 10795

Type strain: Yes

Species: Nocardia elegans

Strain history: CIP <- 2004, A.F. Yassin, Bonn Univ., Bonn, Germany: strain IMMIB N-402 <- 1980, Tsukamura

NCBI tax ID(s): 1210071 (strain), 300029 (species)

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General

@ref: 12175

BacDive-ID: 10795

DSM-Number: 44890

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped, human pathogen

description: Nocardia elegans DSM 44890 is an aerobe, mesophilic, Gram-positive human pathogen that builds an aerial mycelium and was isolated from sputum.

NCBI tax id

NCBI tax idMatching level
300029species
1210071strain

strain history

@refhistory
12175<- A. F. Yassin, IMMIB <- M. Tsukamura (Nocardia nova)
67770IFM 10589 <-- DSM 44890 <-- A. F. Yassin IMMIB N-402 <-- M. Tsukamura (Nocardia nova).
119004CIP <- 2004, A.F. Yassin, Bonn Univ., Bonn, Germany: strain IMMIB N-402 <- 1980, Tsukamura

doi: 10.13145/bacdive10795.20230509.8.1

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 elegans
  • full scientific name: Nocardia elegans Yassin and Brenner 2005

@ref: 12175

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia elegans

full scientific name: Nocardia elegans Yassin and Brenner 2005

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31443positiverod-shapedno
119004positiverod-shapedno

colony morphology

@refcolony colormedium used
69365Deep orange (2011)ISP 2
69365Deep orange (2011)ISP 7
69365Daffodil yellow (1007)ISP 6
69365Pastel yellow (1034)suter with tyrosine
69365Pastel yellow (1034)suter without tyrosine
69365Yellow orange (2000)ISP 3
69365Yellow orange (2000)ISP 4
69365Yellow orange (2000)ISP 5
119004

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69365yesAerial myceliumLight ivory (1015)ISP 2
69365noAerial myceliumISP 3
69365noAerial myceliumISP 4
69365noAerial myceliumISP 5
69365noAerial myceliumISP 6
69365noAerial myceliumISP 7
69365noAerial myceliumsuter with tyrosine
69365noAerial myceliumsuter without tyrosine

pigmentation

@refproductionnamecolor
31443yes
69365noMelanin
69365yessoluble pigmentBeige red (3012)

multimedia

@refmultimedia contentintellectual property rightscaption
12175https://www.dsmz.de/microorganisms/photos/DSM_44890.jpg© Leibniz-Institut DSMZ
69365DSM_44890_image3.jpegHelmholtz-Zentrum für Infektionsforschung GmbHPlates (535, ISP2, ISP3, ISP4, ISP5, ISP7)
69365DSM_44890_image4.jpegHelmholtz-Zentrum für Infektionsforschung GmbHPlates (535, ISP2, ISP3, ISP4, ISP5, ISP7)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12175GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
12175TRYPTICASE 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
40015MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
119004CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
119004CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
12175positivegrowth28mesophilic
31443positivegrowth22-42
31443positiveoptimum32mesophilic
40015positivegrowth30mesophilic
58783positivegrowth26-42
67770positivegrowth28mesophilic
119004positivegrowth25-41
119004nogrowth10psychrophilic
119004nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31443aerobe
58783aerobe
119004obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
69365NaClpositivegrowth0-2.5 %
119004NaClpositivegrowth0-4 %
119004NaClnogrowth6 %
119004NaClnogrowth8 %
119004NaClnogrowth10 %

observation

@refobservation
31443aggregates in chains
67770quinones: MK-8(H6, ω-cycl)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3144330089acetate+carbon source
3144317234glucose+carbon source
314434853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6936522599arabinose-growth
6936562968cellulose-growth
6936528757fructose-growth
6936517234glucose+growth
6936517268inositol-growth
6936537684mannose-growth
6936516634raffinose-growth
6936526546rhamnose-growth
6936517992sucrose-growth
6936518222xylose-growth
11900416947citrate-carbon source
1190044853esculin-hydrolysis
119004606565hippurate+hydrolysis
11900417632nitrate-reduction
11900416301nitrite-reduction
11900417632nitrate-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: 119004
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119004
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11900415688acetoin-
11900417234glucose-

enzymes

@refvalueactivityec
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
119004oxidase-
119004beta-galactosidase-3.2.1.23
119004alcohol dehydrogenase-1.1.1.1
119004gelatinase-
119004amylase-
119004DNase-
119004caseinase-3.4.21.50
119004catalase+1.11.1.6
119004gamma-glutamyltransferase+2.3.2.2
119004lecithinase-
119004lipase-
119004lysine decarboxylase-4.1.1.18
119004ornithine decarboxylase-4.1.1.17
119004phenylalanine ammonia-lyase-4.3.1.24
119004protease-
119004tryptophan deaminase-
119004urease+3.5.1.5
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
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
69365+--+/---+/-------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
69365+/-+/-++++/----++/--+/--+/-+---
119004+++-+--+-++-+-++----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119004------------------------+/-------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119004+----------------+-------------------------------+-------------------------+--+++-------+-+-----+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
12175sputumJapanJPNAsia
58783Human sputumJapanJPNAsia
67770Sputum of a patient with a pulmonary infection
119004SputumJapanJPNAsia1980

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_4800.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_1088;98_1298;99_4800&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: GQ376166
  • Sequence Identity:
  • Total samples: 13
  • soil counts: 7
  • animal counts: 4
  • plant counts: 2

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12175yes, in single cases1Risk group (German classification)
1190042Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia elegans strain DSM 44890 16S ribosomal RNA gene, partial sequenceDQ6599051388ena300029
12175Nocardia elegans partial 16S rRNA gene, type strain IMMIB N-402AJ8540571483ena300029
67770Nocardia elegans 16S ribosomal RNA gene, partial sequenceGQ3761661439ena300029

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia elegans NBRC 1082351210071.4wgspatric1210071
66792Nocardia elegans NBRC 1082352731957731draftimg1210071
67770Nocardia elegans NBRC 108235GCA_001612845contigncbi1210071

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.258no
gram-positiveyes85.749yes
anaerobicno98.63yes
aerobicyes88.072yes
halophileno92.313no
spore-formingyes81.166no
thermophileno99.188yes
glucose-utilyes87.333no
flagellatedno98.496no
glucose-fermentno92.163no

External links

@ref: 12175

culture collection no.: DSM 44890, CCUG 50200, CIP 108553, IMMIB N-402, JCM 13394, JCM 13374, IFM 10589, NBRC 108235

straininfo link

  • @ref: 80060
  • straininfo: 215154

literature

  • topic: Phylogeny
  • Pubmed-ID: 16014473
  • title: Nocardia elegans sp. nov., a member of the Nocardia vaccinii clade isolated from sputum.
  • authors: Yassin AF, Brenner S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63570-0
  • year: 2005
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Humans, Lung Diseases/*microbiology, Molecular Sequence Data, Mycolic Acids/analysis, Nocardia/chemistry/*classification/*genetics/isolation & purification, Nocardia Infections/*microbiology, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sputum/*microbiology
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12175Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44890)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44890
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
31443Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127747
40015Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6188
58783Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50200)https://www.ccug.se/strain?id=50200
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
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69365Wink, J.https://cdn.dsmz.de/wink/DSM%2044890.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
80060Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID215154.1StrainInfo: A central database for resolving microbial strain identifiers
119004Curators of the CIPCollection of Institut Pasteur (CIP 108553)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108553