Strain identifier

BacDive ID: 8476

Type strain: Yes

Species: Mycobacterium novocastrense

Strain Designation: 73

Strain history: CIP <- 1998, M. Goodfellow, Dept. Microbiol., Medical School, Newcastle, United Kingdom: strain 73

NCBI tax ID(s): 59813 (species)

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General

@ref: 11599

BacDive-ID: 8476

DSM-Number: 44203

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, rod-shaped

description: Mycobacterium novocastrense 73 is an obligate aerobe, mesophilic, rod-shaped bacterium that was isolated from skin tissue biopsy.

NCBI tax id

  • NCBI tax id: 59813
  • Matching level: species

strain history

@refhistory
11599<- J.G. Magee, 73
363941998, M. Goodfellow, Dept. Microbiol., Medical School, Newcastle, United Kingdom: strain 73
67770CIP 105546 <-- M. Goodfellow 73.
121366CIP <- 1998, M. Goodfellow, Dept. Microbiol., Medical School, Newcastle, United Kingdom: strain 73

doi: 10.13145/bacdive8476.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Mycobacteriaceae
  • genus: Mycobacterium
  • species: Mycobacterium novocastrense
  • full scientific name: Mycobacterium novocastrense Shojaei et al. 1997

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium novocastrense

@ref: 11599

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium novocastrense

full scientific name: Mycobacterium novocastrense Shojaei et al. 1997

strain designation: 73

type strain: yes

Morphology

cell morphology

  • @ref: 121366
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
20018Rapeseed yellow (1021)10-14 days5006
20018Rapeseed yellow (1021)10-14 daysMB7H10
20018Rapeseed yellow (1021)10-14 daysMB7H11

multimedia

  • @ref: 11599
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44203.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11599MIDDLEBROOK MEDIUM (DSMZ Medium 645)yeshttps://mediadive.dsmz.de/medium/645Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
20018MB7H10yesName: Middlebrook 7H10 (MB7H10) Broth Base Composition: amount in percent Middlebrook 7H10 Agar 1.9% Glycerol 0.5% OADC-Enrichment in ml (NL5633) 10ml Comments: Add broth base and glycerol to ddh2O. Adjust volumes. Autoclave. Cool to 42°C. Add OADC-stock. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria OADC stock solution old broth-name: OADC-Stock Composition: Bovine Serum Albumin, fraction V 5 % 1% Oleic Acid in 0.2N NaOH 5ml Glucose 2 % NaCl 0.85 % Comments: Melt 1% Oleic Acid in 65°C water bath. Dissolve all ingredients in 700ml of ddH2O. Adjust volume to 1L. Filter sterilize and store at 4°C. -To make 1% Oleic Acid in 0.2N NaOH: Dissolve 5g oleic acid (ampule) in 500ml 0.2N NaOH (300ml ddH2O + 20ml NaOH + adjust volume to 500ml). Heat solution to 55°C for oleic acid to melt. Store at -20°C in 50ml aliquots. There is no need to sterilize this. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria
20018MB7H11yesName: Middlebrook 7H11 (MB7H11) Broth Base Composition: Middlebrook 7H11 Agar 2% Glycerol 0.5% OADC-Enrichment 10ml Comments: Add broth base and glycerol to ddH2O. Adjust volumes. Autoclave. Cool to 42°C. Add OADC-Stock. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria OADC stock solution old broth-name: OADC-Stock Composition: Bovine Serum Albumin, fraction V 5 % 1% Oleic Acid in 0.2N NaOH 5ml Glucose 2 % NaCl 0.85 % Comments: Melt 1% Oleic Acid in 65°C water bath. Dissolve all ingredients in 700ml of ddH2O. Adjust volume to 1L. Filter sterilize and store at 4°C. -To make 1% Oleic Acid in 0.2N NaOH: Dissolve 5g oleic acid (ampule) in 500ml 0.2N NaOH (300ml ddH2O + 20ml NaOH + adjust volume to 500ml). Heat solution to 55°C for oleic acid to melt. Store at -20°C in 50ml aliquots. There is no need to sterilize this. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria
200185006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
36394MEDIUM 55 - for Mycobacteriumyes
121366CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
20018positiveoptimum37mesophilic
11599positivegrowth37mesophilic
36394positivegrowth37mesophilic
67770positivegrowth37mesophilic
121366positivegrowth10-37
121366nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121366
  • oxygen tolerance: obligate aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
121366606565hippurate+hydrolysis
12136617632nitrate+reduction
12136616301nitrite-reduction
12136617632nitrate-respiration
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 121366
  • 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
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15
121366oxidase-
121366beta-galactosidase-3.2.1.23
121366gelatinase+/-
121366amylase-
121366DNase-
121366caseinase-3.4.21.50
121366catalase+1.11.1.6
121366tween esterase-
121366gamma-glutamyltransferase-2.3.2.2
121366lecithinase-
121366lipase-
121366urease-3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase+3.4.11.3
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
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
20018-+-+----++-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20018++++++++-++---++---
121366-++-+-+--++---+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121366------------------------------------------------------------+-----------------+---------+-------+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11599skin tissue biopsyUnited KingdomGBREurope
54690Human skin,hand,biopsyUnited KingdomGBREurope
67770Biopsy from a slowly spreading skin granulation on a child
121366Human, Slowly spreading skin granulation of the hand of a child

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Biopsy
#Host Body-Site#Organ#Skin, Nail, Hair

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115992Risk group (German classification)
200182German classification
1213661Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium novocastrense 16S ribosomal RNA gene, complete sequenceU967471517ena59813
20218Mycobacterium novocastrense strain CIP 105546 16S ribosomal RNA gene, partial sequenceAF547953543ena59813

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium novocastrense strain JCM1811459813.3wgspatric59813
67770Mycolicibacterium novocastrense JCM18114GCA_001570485scaffoldncbi59813
66792Mycolicibacterium novocastrense DSM 44203GCA_025822165scaffoldncbi59813

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes89.184no
anaerobicno99.379no
halophileno87.038no
spore-formingno88.639no
glucose-utilyes83.483no
thermophileno99.661no
flagellatedno98.83no
aerobicyes87.812no
motileno93.641no
glucose-fermentno91.483yes

External links

@ref: 11599

culture collection no.: DSM 44203, CCUG 39183, CIP 105546, JCM 18114

straininfo link

  • @ref: 77871
  • straininfo: 50524

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9336929Mycobacterium novocastrense sp. nov., a rapidly growing photochromogenic mycobacterium.Shojaei H, Goodfellow M, Magee JG, Freeman R, Gould FK, Brignall CGInt J Syst Bacteriol10.1099/00207713-47-4-12051997DNA, Bacterial/analysis, Molecular Sequence Data, Mycobacterium/chemistry/*classification/*genetics/growth & development, Mycolic Acids/analysis, Phenotype, Phylogeny, RNA, Ribosomal, 16S/analysis, Sequence Alignment, Sequence Homology, Nucleic AcidGenetics
Phylogeny29058645Two novel species of rapidly growing mycobacteria: Mycobacterium lehmannii sp. nov. and Mycobacterium neumannii sp. nov.Nouioui I, Sangal V, Carro L, Teramoto K, Jando M, Montero-Calasanz MDC, Igual JM, Sutcliffe I, Goodfellow M, Klenk HPInt J Syst Evol Microbiol10.1099/ijsem.0.0023502017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Multilocus Sequence Typing, Mycobacterium/*classification/isolation & purification, Mycolic Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11599Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44203)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44203
20018Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44203.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
36394Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17577
54690Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39183)https://www.ccug.se/strain?id=39183
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
77871Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50524.1StrainInfo: A central database for resolving microbial strain identifiers
121366Curators of the CIPCollection of Institut Pasteur (CIP 105546)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105546