Strain identifier

BacDive ID: 10787

Type strain: Yes

Species: Nocardia pneumoniae

Strain history: CIP <- 2005, JCM <- 2003, IFM

NCBI tax ID(s): 1206737 (strain), 228601 (species)

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General

@ref: 12048

BacDive-ID: 10787

DSM-Number: 44730

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped

description: Nocardia pneumoniae DSM 44730 is an aerobe, spore-forming, mesophilic bacterium that was isolated from human.

NCBI tax id

NCBI tax idMatching level
228601species
1206737strain

strain history

@refhistory
12048<- Y. Mikami, IFM
67770Y. Mikami IFM 0784.
121894CIP <- 2005, JCM <- 2003, IFM

doi: 10.13145/bacdive10787.20250331.9.3

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 pneumoniae
  • full scientific name: Nocardia pneumoniae Kageyama et al. 2004

@ref: 12048

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia pneumoniae

full scientific name: Nocardia pneumoniae Kageyama et al. 2004

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31219positive0.4 µm0.33 µmrod-shapedno
121894positiverod-shapedno
125438positive90.054
125439positive99.2

colony morphology

@refcolony colorincubation periodmedium used
19698Beige10-14 daysISP 2
19698Beige10-14 daysISP 3
1969810-14 daysISP 4
1969810-14 daysISP 5
1969810-14 daysISP 6
19698Beige10-14 daysISP 7
121894

multicellular morphology

@refforms multicellular complexmedium name
19698noISP 2
19698noISP 3
19698noISP 4
19698noISP 5
19698noISP 6
19698noISP 7

pigmentation

  • @ref: 31219
  • production: no

multimedia

  • @ref: 12048
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44730.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12048TRYPTICASE 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
19698ISP 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
19698ISP 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:
19698ISP 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
19698ISP 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
19698ISP 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
19698ISP 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
40047MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121894CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121894CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperature
12048positivegrowth28
19698positiveoptimum28
40047positivegrowth30
67770positivegrowth28
121894positivegrowth10-37
121894nogrowth41
121894nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31219aerobe
121894obligate aerobe
125439obligate aerobe99.3

halophily

@refsaltgrowthtested relationconcentration
121894NaClpositivegrowth0-2 %
121894NaClnogrowth4 %
121894NaClnogrowth6 %
121894NaClnogrowth8 %
121894NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1969817234glucose+
1969822599arabinose-
1969817992sucrose+
1969818222xylose-
1969817268myo-inositol-
1969829864mannitol-
1969828757fructose+
1969826546rhamnose+/-
1969816634raffinose-
1969862968cellulose+/-
3121930089acetate+carbon source
3121916947citrate+carbon source
3121917234glucose+carbon source
312194853esculin+hydrolysis
3121917632nitrate+reduction
6837917992sucrose-fermentation
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
12189416947citrate-carbon source
1218944853esculin+hydrolysis
121894606565hippurate+hydrolysis
12189417632nitrate+reduction
12189416301nitrite-reduction
12189417632nitrate-respiration

antibiotic resistance

  • @ref: 121894
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 121894
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12189415688acetoin-
12189417234glucose-

enzymes

@refvalueactivityec
31219arylsulfatase+3.1.6.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121894oxidase-
121894beta-galactosidase+3.2.1.23
121894alcohol dehydrogenase-1.1.1.1
121894gelatinase+
121894amylase-
121894DNase-
121894caseinase-3.4.21.50
121894catalase+1.11.1.6
121894tween esterase-
121894gamma-glutamyltransferase-2.3.2.2
121894lecithinase-
121894lipase-
121894lysine decarboxylase-4.1.1.18
121894ornithine decarboxylase-4.1.1.17
121894phenylalanine ammonia-lyase-4.3.1.24
121894tryptophan deaminase-
121894urease-3.5.1.5
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68382alpha-galactosidase-3.2.1.22
68379gelatinase+
68379urease+3.5.1.5
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

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
19698--+--+-+/-++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19698+++-++++-++---++---
121894+++-+--+-++-+-++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121894-+-----------------------------+-----------------++--+----++--------------++--+++-------+-+----++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12048humanJapanJPNAsia
67770SputumJapanJPNAsia
121894Human, SputumJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Human

taxonmaps

  • @ref: 69479
  • File name: preview.99_7936.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_907;98_5793;99_7936&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: GQ853075
  • Sequence Identity:
  • Total samples: 10
  • soil counts: 5
  • aquatic counts: 3
  • animal counts: 1
  • plant counts: 1

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12048yes, in single cases1Risk group (German classification)
1218942Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia pneumoniae strain DSM 44730 isolate VNS40 16S ribosomal RNA gene, partial sequenceAY903622606nuccore228601
20218Nocardia pneumoniae strain DSM 44730 16S ribosomal RNA gene, partial sequenceJF7973131414nuccore228601
20218Nocardia pneumoniae strain DSM 44730 16S ribosomal RNA gene, partial sequenceJN041465462nuccore228601
20218Nocardia pneumoniae strain W9813 16S ribosomal RNA gene, partial sequenceGQ8530751441nuccore228601
31219Nocardia pneumoniae gene for 16S rRNA, partial sequenceAB1087801453nuccore228601

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia pneumoniae NBRC 1001361206737.4wgspatric1206737
66792Nocardia pneumoniae NBRC 1001362551306160draftimg1206737
67770Nocardia pneumoniae NBRC 100136GCA_000308755contigncbi1206737

GC content

@refGC-contentmethod
3121968
6777068.1genome sequence analysis
6777068high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes90.054yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.901yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes62.921no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.741yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96yes
125438motile2+flagellatedAbility to perform flagellated movementno89no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes76.7
125439BacteriaNetmotilityAbility to perform movementno89.1
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.2
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.3

External links

@ref: 12048

culture collection no.: DSM 44730, IFM 0784, JCM 12119, NBRC 100136, CIP 108644

straininfo link

  • @ref: 80052
  • straininfo: 131105

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545428Nocardia araoensis sp. nov. and Nocardia pneumoniae sp. nov., isolated from patients in Japan.Kageyama A, Yazawa K, Mukai A, Kohara T, Nishimura K, Kroppenstedt RM, Mikami YInt J Syst Evol Microbiol10.1099/ijs.0.63074-02004Aged, Bacterial Typing Techniques, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Humans, Japan, Lung/microbiology, Male, Molecular Sequence Data, Nocardia/*classification/cytology/*isolation & purification/physiology, Nocardia Infections/*microbiology, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
Phylogeny20348315Nocardia niwae sp. nov., isolated from human pulmonary sources.Moser BD, Klenk HP, Schumann P, Potter G, Lasker BA, Steigerwalt AG, Hinrikson HP, Brown JMInt J Syst Evol Microbiol10.1099/ijs.0.020370-02010Adult, Aged, Aged, 80 and over, Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, DNA Gyrase/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Female, Florida, Humans, Lung/*microbiology, Male, Microbial Sensitivity Tests, Middle Aged, Molecular Sequence Data, Nocardia/*classification/drug effects/genetics/isolation & purification, Nocardia Infections/*microbiology, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12048Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44730)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44730
19698Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44730.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
31219Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127545
40047Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6296
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
80052Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131105.1StrainInfo: A central database for resolving microbial strain identifiers
121894Curators of the CIPCollection of Institut Pasteur (CIP 108644)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108644
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1