Strain identifier

BacDive ID: 10798

Type strain: Yes

Species: Nocardia anaemiae

Strain history: CIP <- 2005, JCM <- 2004, Y. Mikami, Chiba, Japan: strain IFM 0323

NCBI tax ID(s): 1210065 (strain), 263910 (species)

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General

@ref: 12117

BacDive-ID: 10798

DSM-Number: 44821

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

description: Nocardia anaemiae DSM 44821 is an obligate aerobe, spore-forming, mesophilic human pathogen that builds an aerial mycelium and was isolated from human.

NCBI tax id

NCBI tax idMatching level
1210065strain
263910species

strain history

@refhistory
12117<- Y. Mikami, IFM
67770Y. Mikami IFM 0323.
116368CIP <- 2005, JCM <- 2004, Y. Mikami, Chiba, Japan: strain IFM 0323

doi: 10.13145/bacdive10798.20230509.8.1

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 anaemiae
  • full scientific name: Nocardia anaemiae Kageyama et al. 2005

@ref: 12117

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia anaemiae

full scientific name: Nocardia anaemiae Kageyama et al. 2005

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.682
69480100positive
116368nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19710Cream10-14 daysISP 2
19710Cream10-14 daysISP 3
19710Cream10-14 daysISP 4
19710Light lemon yellow10-14 daysISP 5
19710Cream10-14 daysISP 6
19710Platinum grey10-14 daysISP 7
116368

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19710noISP 2
19710noISP 3
19710noISP 4
19710yesISP 5Aerial MyceliumCream
19710noISP 6
19710noISP 7

multimedia

  • @ref: 12117
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44821.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12117TRYPTICASE 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
12117GYM 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
19710ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19710ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19710ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19710ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19710ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19710ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
38349MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116368CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
12117positivegrowth28mesophilic
19710positiveoptimum28mesophilic
38349positivegrowth30mesophilic
67770positivegrowth28mesophilic
116368positivegrowth25-41
116368nogrowth10psychrophilic
116368nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116368
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes98
69480no99.339

halophily

@refsaltgrowthtested relationconcentration
116368NaClpositivegrowth0-6 %
116368NaClnogrowth8 %
116368NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1971017234glucose+
1971022599arabinose+
1971017992sucrose-
1971018222xylose-
1971017268myo-inositol-
1971029864mannitol+
1971028757fructose+
1971026546rhamnose-
1971016634raffinose-
1971062968cellulose-
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
683714853esculin+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
11636816947citrate-carbon source
1163684853esculin-hydrolysis
116368606565hippurate+hydrolysis
11636817632nitrate+reduction
11636816301nitrite-reduction
11636817632nitrate-respiration
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation

metabolite production

  • @ref: 116368
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11636815688acetoin-
11636817234glucose-

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
116368oxidase-
116368beta-galactosidase-3.2.1.23
116368alcohol dehydrogenase-1.1.1.1
116368gelatinase+/-
116368amylase-
116368DNase-
116368caseinase-3.4.21.50
116368catalase+1.11.1.6
116368tween esterase-
116368gamma-glutamyltransferase-2.3.2.2
116368lecithinase-
116368lipase-
116368lysine decarboxylase-4.1.1.18
116368ornithine decarboxylase-4.1.1.17
116368phenylalanine ammonia-lyase-4.3.1.24
116368tryptophan deaminase-
116368urease+3.5.1.5
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
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

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
19710--+--+-----

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19710+++-+--+-++---++---
116368----++-+-+----+-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116368+/----------+++----------+/-++/--+--++-+----++---------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12117humanJapanJPNAsia
6777073-Year-old Japanese male patient
116368HumanJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Human

taxonmaps

  • @ref: 69479
  • File name: preview.99_5891.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_1916;98_4380;99_5891&stattab=map
  • Last taxonomy: Nocardia anaemiae subclade
  • 16S sequence: GQ376192
  • Sequence Identity:
  • Total samples: 169
  • soil counts: 142
  • aquatic counts: 4
  • animal counts: 13
  • plant counts: 10

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12117yes, in single cases1Risk group (German classification)
197102Risk group (German classification)
1163682Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia anaemiae 16S ribosomal RNA gene, partial sequenceGQ3761921441ena263910
20218Nocardia anaemiae strain DSM 44821 16S ribosomal RNA gene, partial sequenceJF7973041414ena263910
20218Nocardia anaemiae strain DSM 44821 16S ribosomal RNA gene, partial sequenceJN041532462ena263910
20218Nocardia sp. IFM 0323 gene for 16S rRNA, partial sequence, strain:IFM 0323AB1628011498ena263910

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia anaemiae NBRC 1004621210065.4wgspatric1210065
66792Nocardia anaemiae NBRC 1004622731957725draftimg1210065
67770Nocardia anaemiae NBRC 100462GCA_001612725contigncbi1210065

GC content

  • @ref: 67770
  • GC-content: 66.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes98no
motileno92.713no
gram-positiveyes87.879no
anaerobicno99.185no
aerobicyes91.864no
halophileno95.615no
spore-formingyes85.389no
glucose-utilyes89.483yes
flagellatedno98.163no
thermophileno99.291no
glucose-fermentno90.794no

External links

@ref: 12117

culture collection no.: DSM 44821, IFM 0323, JCM 12396, NBRC 100462, CIP 108869

straininfo link

  • @ref: 80063
  • straininfo: 200537

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15711532Nocardia anaemiae sp. nov. isolated from an immunocompromised patient and the first isolation report of Nocardia vinacea from humans.Kageyama A, Yazawa K, Nishimura K, Mikami YNihon Ishinkin Gakkai Zasshi10.3314/jjmm.46.212005DNA, Ribosomal/analysis, Humans, *Immunocompromised Host, Nocardia/*classification/genetics/*isolation & purification, Nocardia Infections/*microbiology, Phenotype, PhylogenyPathogenicity
Pathogenicity35450515Identification of a novel drug-resistant community-acquired Nocardia spp. in a patient with bronchiectasis.Li Z, Li Y, Li S, Li Z, Mai Y, Cheng J, Su D, Zhan Y, Zhong N, Ye FEmerg Microbes Infect10.1080/22221751.2022.20695142022Animals, *Bronchiectasis/epidemiology, Humans, Immunocompromised Host, Mice, *Nocardia/genetics, *Nocardia Infections/drug therapy/epidemiology, *Pneumonia

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12117Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44821)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44821
19710Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44821.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
38349Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6546
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
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
80063Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID200537.1StrainInfo: A central database for resolving microbial strain identifiers
116368Curators of the CIPCollection of Institut Pasteur (CIP 108869)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108869