Strain identifier

BacDive ID: 10782

Type strain: Yes

Species: Nocardia inohanensis

Strain history: CIP <- 2004, DSMZ <- Y. Mikami, Chiba, Japan: strain IFM 0092

NCBI tax ID(s): 1210077 (strain), 209246 (species)

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General

@ref: 11863

BacDive-ID: 10782

DSM-Number: 44667

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

description: Nocardia inohanensis DSM 44667 is a spore-forming, mesophilic, Gram-positive human pathogen that was isolated from human.

NCBI tax id

NCBI tax idMatching level
1210077strain
209246species

strain history

@refhistory
11863<- Y. Mikami; IFM 0092
67770Y. Mikami IFM 0092 <-- A. González Ochoa.
120132CIP <- 2004, DSMZ <- Y. Mikami, Chiba, Japan: strain IFM 0092

doi: 10.13145/bacdive10782.20230509.8.1

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

@ref: 11863

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia inohanensis

full scientific name: Nocardia inohanensis Kageyama et al. 2004 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29989positiverod-shapedno
69480no91.683
69480positive100
120132positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
20088Saffron yellow (1017)10-14 daysISP 2
20088Saffron yellow (1017)10-14 daysISP 3
20088Saffron yellow (1017)10-14 daysISP 4
20088Saffron yellow (1017)10-14 daysISP 5
20088Saffron yellow (1017)10-14 daysISP 6
20088Saffron yellow (1017)10-14 daysISP 7
120132

multicellular morphology

@refforms multicellular complexmedium name
20088noISP 2
20088noISP 3
20088noISP 4
20088noISP 5
20088noISP 6
20088noISP 7

pigmentation

  • @ref: 29989
  • production: no

multimedia

  • @ref: 11863
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44667.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11863GPHF-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
11863GYM 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
20088ISP 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
20088ISP 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:
20088ISP 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
20088ISP 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
20088ISP 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
20088ISP 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
39999MEDIUM 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)
120132CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11863positivegrowth28mesophilic
20088positiveoptimum28mesophilic
29989positiveoptimum37mesophilic
39999positivegrowth30mesophilic
67770positivegrowth28mesophilic
120132positivegrowth30-41
120132nogrowth10psychrophilic
120132nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480no90.403

halophily

@refsaltgrowthtested relationconcentration
120132NaClpositivegrowth0-4 %
120132NaClnogrowth6 %
120132NaClnogrowth8 %
120132NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2008817234glucose+
2008822599arabinose-
2008817992sucrose-
2008818222xylose-
2008817268myo-inositol-
2008829864mannitol-
2008828757fructose-
2008826546rhamnose-
2008816634raffinose-
2008862968cellulose+
2998916947citrate+carbon source
2998917234glucose+carbon source
2998937684mannose+carbon source
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
12013216947citrate-carbon source
1201324853esculin-hydrolysis
120132606565hippurate-hydrolysis
12013217632nitrate+reduction
12013216301nitrite-reduction
12013217632nitrate-respiration
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation

metabolite production

  • @ref: 120132
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12013215688acetoin-
12013217234glucose-

enzymes

@refvalueactivityec
29989urease+3.5.1.5
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
120132oxidase-
120132beta-galactosidase+3.2.1.23
120132alcohol dehydrogenase-1.1.1.1
120132gelatinase-
120132amylase-
120132DNase-
120132caseinase-3.4.21.50
120132catalase+1.11.1.6
120132tween esterase-
120132gamma-glutamyltransferase-2.3.2.2
120132lecithinase-
120132lipase-
120132lysine decarboxylase-4.1.1.18
120132ornithine decarboxylase-4.1.1.17
120132phenylalanine ammonia-lyase-4.3.1.24
120132protease-
120132tryptophan deaminase-
120132urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
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
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
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

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
20088+-+--+-+---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20088+++-++---++---++---
120132+++-+----++---++----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120132------------------------+/-------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11863humanMexicoMEXNorth America
67770Patient in Mexico
120132HumanMexicoMEXNorth America

isolation source categories

  • Cat1: #Host
  • Cat2: #Human

taxonmaps

  • @ref: 69479
  • File name: preview.99_866.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_448;98_685;99_866&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: GQ376173
  • Sequence Identity:
  • Total samples: 287
  • soil counts: 266
  • aquatic counts: 9
  • animal counts: 7
  • plant counts: 5

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
11863yes, in single cases1Risk group (German classification)
200882German classification
1201322Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia inohanensis strain DSM 44667 isolate VNS30 16S ribosomal RNA gene, partial sequenceAY903611606ena209246
20218Nocardia inohanensis strain DSM 44667 16S ribosomal RNA gene, partial sequenceDQ6599081363ena209246
20218Nocardia inohanensis 16S ribosomal RNA gene, partial sequenceGQ3761731362ena209246
11863Nocardia inohanensis gene for 16S rRNA, partial sequence, strain:IFM 0092AB0925601442ena209246

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia inohanensis NBRC 1001281210077.4wgspatric1210077
66792Nocardia inohanensis NBRC 1001282731957736draftimg1210077
67770Nocardia inohanensis NBRC 100128GCA_001612945contigncbi1210077

GC content

@refGC-contentmethod
1186369.3
6777067.8genome sequence analysis
6777069.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.844no
gram-positiveyes92.72no
anaerobicno99.6no
aerobicyes93.614no
halophileno93.76no
spore-formingyes87.231no
thermophileno99.577yes
glucose-utilyes88.848no
flagellatedno97.839yes
glucose-fermentno89.439no

External links

@ref: 11863

culture collection no.: DSM 44667, JCM 11891, NBRC 100128, IFM 0092, CIP 108421

straininfo link

  • @ref: 80048
  • straininfo: 131426

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023976Nocardia inohanensis sp. nov., Nocardia yamanashiensis sp. nov. and Nocardia niigatensis sp. nov., isolated from clinical specimens.Kageyama A, Yazawa K, Nishimura K, Mikami YInt J Syst Evol Microbiol10.1099/ijs.0.02794-02004Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Humans, Microscopy, Electron, Scanning, Molecular Sequence Data, Nocardia/*classification/genetics/isolation & purification/ultrastructure, Nocardia Infections/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsPathogenicity
Phylogeny31339486Nocardia yunnanensis sp. nov., an actinomycete isolated from a soil sample.Zhang JX, Ming H, Zhao ZL, Ji WL, Chang XL, Zhang LY, Cheng LJ, Meng XL, Li WJ, Nie GXInt J Syst Evol Microbiol10.1099/ijsem.0.0036002019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nocardia/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
11863Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44667)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44667
20088Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44667.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
29989Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126356
39999Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6042
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
80048Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131426.1StrainInfo: A central database for resolving microbial strain identifiers
120132Curators of the CIPCollection of Institut Pasteur (CIP 108421)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108421