Strain identifier

BacDive ID: 10731

Type strain: Yes

Species: Nocardia abscessus

Strain Designation: VA-12

Strain history: CIP <- 2000, JCM <- DSMZ <- AF Yassin IMMIB D-1592

NCBI tax ID(s): 1206723 (strain), 120957 (species)

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General

@ref: 11743

BacDive-ID: 10731

DSM-Number: 44432

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

description: Nocardia abscessus VA-12 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from joint abscess of a 56 year old man with a complete endoprosthesis of one of his knees.

NCBI tax id

NCBI tax idMatching level
1206723strain
120957species

strain history

@refhistory
11743<- A. F. Yassin; IMMIB D-1592 <- Inst. of Medical Microbiology, Hannover
338102002, H. Marchandin, Montpellier, France: strain B1162
67770DSM 44432 <-- A. F. Yassin IMMIB D-1592.
115982CIP <- 2000, JCM <- DSMZ <- AF Yassin IMMIB D-1592

doi: 10.13145/bacdive10731.20230509.8.1

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 abscessus
  • full scientific name: Nocardia abscessus Yassin et al. 2000

@ref: 11743

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia abscessus

full scientific name: Nocardia abscessus Yassin et al. 2000

strain designation: VA-12

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.128
69480100positive
115982nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20058Colorless10-14 daysISP 2
20058Colorless10-14 daysISP 3
20058Colorless10-14 daysISP 4
20058Colorless10-14 daysISP 5
20058Colorless10-14 daysISP 6
20058Colorless10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20058yesAerial MyceliumWhiteISP 2
20058yesAerial MyceliumWhiteISP 3
20058noISP 4
20058yesAerial MyceliumWhiteISP 5
20058yesAerial MyceliumISP 6
20058yesAerial MyceliumWhiteISP 7

multimedia

  • @ref: 11743
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44432.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11743GPHF-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
11743GYM 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
20058ISP 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
20058ISP 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:
20058ISP 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
20058ISP 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
20058ISP 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
20058ISP 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
33810MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
39591MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
115982CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57
115982CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
20058positiveoptimum28mesophilic
11743positivegrowth28mesophilic
33810positivegrowth37mesophilic
39591positivegrowth30mesophilic
56995positivegrowth30mesophilic
67770positivegrowth28mesophilic
115982positivegrowth25-37mesophilic
115982nogrowth10psychrophilic
115982nogrowth41thermophilic
115982nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
56995aerobe
115982obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 90

halophily

@refsaltgrowthtested relationconcentration
115982NaClpositivegrowth0-2 %
115982NaClnogrowth4 %
115982NaClnogrowth6 %
115982NaClnogrowth8 %
115982NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H6, ω-cycl), epoxy-MK-8(H6, ω-cycl)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11598216947citrate-carbon source
1159824853esculin+hydrolysis
115982606565hippurate+hydrolysis
11598217632nitrate+reduction
11598216301nitrite-reduction
11598217632nitrate-respiration
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 115982
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11598215688acetoin-
11598217234glucose-

enzymes

@refvalueactivityec
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
115982oxidase-
115982beta-galactosidase-3.2.1.23
115982alcohol dehydrogenase-1.1.1.1
115982gelatinase+/-
115982amylase-
115982DNase-
115982caseinase-3.4.21.50
115982catalase+1.11.1.6
115982tween esterase-
115982gamma-glutamyltransferase-2.3.2.2
115982lecithinase-
115982lipase-
115982lysine decarboxylase-4.1.1.18
115982ornithine decarboxylase-4.1.1.17
115982phenylalanine ammonia-lyase-4.3.1.24
115982protease-
115982tryptophan deaminase-
115982urease-3.5.1.5
68382lipase (C 14)-
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
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

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20058-+-+--+-+-+/---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20058+++-+++++++--+++---
115982---------++---+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
115982+----------------------+-------+-----------+-----++--+---------------------+---++-------+-+----++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
11743joint abscess of a 56 year old man with a complete endoprosthesis of one of his kneesHannoverGermanyDEUEurope52.37059.7332
56995Human abscess
67770Joint abscess of a 56-year-old male patient with a complete endoprosthesis in one of his knees
115982Human, Abscess

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body-Site#Other#Abscess
#Host Body-Site#Limb#Joint
#Host Body-Site#Limb#Leg
#Host#Human#Male

taxonmaps

  • @ref: 69479
  • File name: preview.99_5901.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_280;98_312;99_5901&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: GQ376194
  • Sequence Identity:
  • Total samples: 14
  • soil counts: 9
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
117432Risk group (German classification)
200582German classification
1159822Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia asteroides clone A1 16S ribosomal RNA gene, partial sequenceAY262328500ena1824
20218Nocardia abscessus strain DSM 44432 16S ribosomal RNA gene, partial sequenceAY544980606ena1206723
20218Nocardia abscessus strain ATCC BAA-279 16S ribosomal RNA gene, partial sequenceDQ6598951400ena1206723
20218Nocardia abscessus NBRC 100374 16S ribosomal RNA gene, partial sequenceGQ3761941441ena1206723
20218Nocardia abscessus strain ATCC BAA-279 clone 1 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236316644ena1206723
20218Nocardia abscessus strain ATCC BAA-279 clone 2 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236317644ena1206723
20218Nocardia abscessus strain ATCC BAA-279 clone 3 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236318644ena1206723
20218Nocardia abscessus strain ATCC BAA-279 clone 4 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236319644ena1206723
20218Nocardia abscessus strain ATCC BAA-279 clone 5 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236320644ena1206723
20218Nocardia abscessus NBRC 100374 strain DSM 44432 16S ribosomal RNA gene, partial sequenceJN041489462ena1206723
20218N.asteroides 16S rRNA gene (ATCC 23824)X848511412ena1824
11743Nocardia abscessus strain IMMIB D-1592T 16S ribosomal RNA gene, partial sequenceAF2182921457ena1206723

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia abscessus NBRC 1003741206723.4wgspatric1206723
66792Nocardia abscessus NBRC 1003742551306170draftimg1206723
67770Nocardia abscessus NBRC 100374GCA_000308455contigncbi1206723

GC content

@refGC-contentmethod
6777068.2genome sequence analysis
6777067.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes90no
motileno93.709no
gram-positiveyes84.771no
anaerobicno98.787no
aerobicyes90.028yes
halophileno94.424no
spore-formingyes87.975no
glucose-utilyes87.818no
flagellatedno97.972no
thermophileno98.795yes
glucose-fermentno92.899yes

External links

@ref: 11743

culture collection no.: DSM 44432, ATCC 23824, ATCC BAA 279, IMMIB D-1599, IMMIB N-63, JCM 10984, NBRC 100374, CCUG 45938, CIP 106822, IMMIB D-1592, CGMCC 4.1723, IFM 10029

straininfo link

  • @ref: 79999
  • straininfo: 46629

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10939654Nocardia abscessus sp. nov.Yassin AF, Rainey FA, Mendrock U, Brzezinka H, Schaal KPInt J Syst Evol Microbiol10.1099/00207713-50-4-14872000Adult, Cloning, Molecular, DNA, Bacterial/genetics, Genes, Bacterial, Humans, Male, Middle Aged, Molecular Sequence Data, Nocardia/chemistry/*classification/genetics, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/analysis, RNA, Ribosomal, 16S/analysisEnzymology
Phylogeny28112922Nabscessins A and B, Aminocyclitol Derivatives from Nocardia abscessus IFM 10029(T).Hara S, Ishikawa N, Hara Y, Nehira T, Sakai K, Gonoi T, Ishibashi MJ Nat Prod10.1021/acs.jnatprod.6b009352017Actinobacteria/chemistry, Antifungal Agents/chemistry/*isolation & purification/*pharmacology, Cryptococcus neoformans/drug effects, Cyclitols/chemistry/*isolation & purification, Microbial Sensitivity Tests, Molecular Structure, Nocardia/*chemistry, Phylogeny, RNA, Ribosomal, 16S/chemistryEnzymology
Metabolism30270243Isolation of Nabscessin C from Nocardia abscessus IFM 10029(T) and a Study on Biosynthetic Pathway for Nabscessins.Hara S, Hara Y, Arai MA, Kusuya Y, Takahashi H, Yaguchi T, Ishibashi MChem Pharm Bull (Tokyo)10.1248/cpb.c18-004302018Acetylation, Animals, Cell Line, Cell Proliferation, Cyclitols/chemistry/isolation & purification/*metabolism, Hydrolysis, Mice, Molecular Structure, Nocardia asteroides/*chemistry/metabolism, Seeds/chemistry/metabolismPhylogeny
Phylogeny33019781Genomic Virulence Features of Two Novel Species Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., Isolated from Patients with Chronic Pulmonary Diseases.Nouioui I, Cortes-Albayay C, Neumann-Schaal M, Vicente D, Cilla G, Klenk HP, Marimon JM, Ercibengoa MMicroorganisms10.3390/microorganisms81015172020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11743Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44432)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44432
20058Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44432.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
33810Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4937
39591Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18995
56995Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45938)https://www.ccug.se/strain?id=45938
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
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
79999Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46629.1StrainInfo: A central database for resolving microbial strain identifiers
115982Curators of the CIPCollection of Institut Pasteur (CIP 106822)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106822