Strain identifier

BacDive ID: 10753

Type strain: Yes

Species: Nocardia africana

Strain Designation: SD769

Strain history: CIP <- 2005, DSMZ <- M. Goodfellow, Newcastle Univ., Newcastle upon Tyne, UK: strain SD769

NCBI tax ID(s): 1210061 (strain), 134964 (species)

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General

@ref: 11817

BacDive-ID: 10753

DSM-Number: 44491

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, human pathogen

description: Nocardia africana SD769 is an aerobe, mesophilic human pathogen that builds an aerial mycelium and was isolated from sputa from patient.

NCBI tax id

NCBI tax idMatching level
134964species
1210061strain

strain history

@refhistory
11817<- M. Goodfellow; SD769 <- M. E. Hamid; {2000}
67770NCTC 13181 <-- M. Goodfellow SD769.
116104CIP <- 2005, DSMZ <- M. Goodfellow, Newcastle Univ., Newcastle upon Tyne, UK: strain SD769

doi: 10.13145/bacdive10753.20230509.8.1

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 africana
  • full scientific name: Nocardia africana Hamid et al. 2001

@ref: 11817

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia africana

full scientific name: Nocardia africana Hamid et al. 2001 emend. Nouioui et al. 2018

strain designation: SD769

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.62
69480100positive
116104nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20065Pastel orange (2003)10-14 daysISP 2
20065Pastel orange (2003)10-14 daysISP 3
20065Pastel orange (2003)10-14 daysISP 4
20065Pastel orange (2003)10-14 daysISP 5
20065Pastel orange (2003)10-14 daysISP 6
20065Pastel orange (2003)10-14 daysISP 7
116104

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20065yesAerial MyceliumWhiteISP 2
20065yesAerial MyceliumWhiteISP 3
20065noISP 4
20065noISP 5
20065noISP 6
20065noISP 7

multimedia

  • @ref: 11817
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44491.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11817TRYPTICASE 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
11817GYM 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
20065ISP 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
20065ISP 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:
20065ISP 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
20065ISP 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
20065ISP 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
20065ISP 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
37462MEDIUM 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)
116104CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57
116104CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
20065positiveoptimum28mesophilic
11817positivegrowth28mesophilic
37462positivegrowth30mesophilic
57071positivegrowth28-37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57071aerobe
116104obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.148

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
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
68371D-lyxose-builds acid from62318
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
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
116104nitrate+reduction17632
116104nitrite-reduction16301
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

metabolite production

  • @ref: 116104
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
116104oxidase-
116104alcohol dehydrogenase-1.1.1.1
116104catalase+1.11.1.6
116104lysine decarboxylase-4.1.1.18
116104ornithine decarboxylase-4.1.1.17
116104urease-3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382naphthol-AS-BI-phosphohydrolase+
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
20065--++/-----+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20065-+++++++--+----+---
116104+++-++++-++-+-++----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116104+--+++---++++----+-+/-++++++++++++------++-+----+/---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
11817sputa from patientSudanSDNAfrica
57071Human sputumSudanSDNAfrica2000
67770Sputum of a patient with pulmonary diseaseSudanSDNAfrica
116104Human, SputumSudanSDNAfrica

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Fluids#Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_1641.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_1088;98_1298;99_1641&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: AY089701
  • Sequence Identity:
  • Total samples: 4172
  • soil counts: 2461
  • aquatic counts: 606
  • animal counts: 719
  • plant counts: 386

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
11817yesyes2Risk group (German classification)
200652German classification
1161042Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia africana strain DSM 44491 16S ribosomal RNA gene, complete sequenceAF4300541492ena134964
20218Nocardia africana strain DSM 44491 note copy 1 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536392329ena134964
20218Nocardia africana strain DSM 44491 16S ribosomal RNA, partial sequenceAY0897011371ena134964
20218Nocardia africana strain DSM 44491 16S ribosomal RNA gene, partial sequenceAY756540606ena134964
20218Nocardia africana 16S ribosomal RNA gene, partial sequenceGQ3761571439ena134964
20218Nocardia africana strain DSM 44491 16S ribosomal RNA gene, partial sequenceJN041605462ena134964
11817Nocardia africana 16S ribosomal RNA gene, partial sequenceAF2771981469ena134964

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia africana NBRC 1003791210061.4wgspatric1210061
66792Nocardia africana NBRC 1003792731957722draftimg1210061
67770Nocardia africana NBRC 100379GCA_001612635contigncbi1210061

GC content

  • @ref: 67770
  • GC-content: 67.9
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes87no
motileno92.531no
gram-positiveyes87.844no
anaerobicno98.859no
aerobicyes89.135yes
halophileno93.85no
spore-formingyes82.872no
glucose-utilyes88.93no
flagellatedno98.392no
thermophileno98.606no
glucose-fermentno92.377yes

External links

@ref: 11817

culture collection no.: CCUG 46122, DSM 44491, ATCC BAA 280, CIP 109047, NBRC 100379, NCTC 13181, JCM 11438

straininfo link

  • @ref: 80021
  • straininfo: 50653

literature

  • topic: Phylogeny
  • Pubmed-ID: 32897850
  • title: Nocardia aurantiaca sp. nov., isolated from soil in Thailand.
  • authors: Kanchanasin P, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W, Tanasupawat S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.004432
  • year: 2020
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nocardia/*classification/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11817Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44491)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44491
20065Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44491.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
37462Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6745
57071Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46122)https://www.ccug.se/strain?id=46122
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)
80021Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50653.1StrainInfo: A central database for resolving microbial strain identifiers
116104Curators of the CIPCollection of Institut Pasteur (CIP 109047)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109047