Strain identifier

BacDive ID: 8469

Type strain: Yes

Species: Mycobacterium rhodesiae

Strain Designation: 2002

Strain history: CIP <- 2000, JCM <- M. Tsukamura: strain 02002 <- N..F.F. Gane and L. King

NCBI tax ID(s): 36814 (species)

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General

@ref: 11607

BacDive-ID: 8469

DSM-Number: 44223

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, human pathogen

description: Mycobacterium rhodesiae 2002 is an obligate aerobe, mesophilic, Gram-positive human pathogen that was isolated from sputum of a patient with lung tuberculosis.

NCBI tax id

  • NCBI tax id: 36814
  • Matching level: species

strain history

@refhistory
11607<- M. Goodfellow, OI-RHO <- NCTC <- M. Tsukamura, 02002 <- L. King
67770M. Tsukamura 02002 <-- N. F. F. Gane and L. King.
122216CIP <- 2000, JCM <- M. Tsukamura: strain 02002 <- N..F.F. Gane and L. King

doi: 10.13145/bacdive8469.20230509.8.1

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 rhodesiae
  • full scientific name: Mycobacterium rhodesiae (ex Tsukamura et al. 1971) Tsukamura 1981

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium rhodesiae

@ref: 11607

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium rhodesiae

full scientific name: Mycobacterium rhodesiae (ex Tsukamura et al. 1971) Tsukamura 1981 emend. Nouioui et al. 2018

strain designation: 2002

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shape
69480positive100
122216rod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19853Sun yellow10-14 days5006
19853Sun yellow10-14 daysMB7H10
19853Sun yellow10-14 daysMB7H11

multimedia

  • @ref: 11607
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44223.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11607LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354)yeshttps://mediadive.dsmz.de/medium/354Name: LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354) Composition: Potato flour 18.6104 g/l L-Asparagin 2.23325 g/l KH2PO4 1.55087 g/l Mg-citrate 0.372208 g/l Malachite green 0.248139 g/l MgSO4 0.148883 g/l Glycerol Fresh egg mixture Distilled water
11607MIDDLEBROOK 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
19853MB7H10yesName: 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
19853MB7H11yesName: 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
198535006yesMedium: 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
36313MEDIUM 55 - for Mycobacteriumyes
122216CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
19853positiveoptimum37mesophilic
11607positivegrowth37mesophilic
36313positivegrowth37mesophilic
67770positivegrowth37mesophilic
122216positivegrowth22-30
122216nogrowth10psychrophilic
122216nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122216
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no93
69480no99.974

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
122216606565hippurate+hydrolysis
12221617632nitrate-reduction
12221616301nitrite-reduction
12221617632nitrate-respiration
6837917632nitrate-reduction
683794853esculin-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: 122216
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68379gelatinase+
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
122216oxidase-
122216beta-galactosidase-3.2.1.23
122216gelatinase-
122216catalase+1.11.1.6
122216gamma-glutamyltransferase+2.3.2.2
122216urease+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
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

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19853-+-+-----+/-+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19853+++++---+++---+----
122216++++++---++---+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11607sputum of a patient with lung tuberculosisRhodesiaZimbabweZWEAfrica
53792Human sputa,pulmonary diseaseZimbabweZWEAfrica
67770Sputa of a patient with pulmonary diseaseZimbabweZWEAfrica
122216Human, SputumZimbabweZWEAfrica

isolation source categories

Cat1Cat2Cat3
#Infection#Disease#Tuberculosis
#Infection#Patient
#Host Body-Site#Oral cavity and airways#Lung
#Host Body Product#Fluids#Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_2774.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_115;97_219;98_419;99_2774&stattab=map
  • Last taxonomy: Mycolicibacterium
  • 16S sequence: AJ429047
  • Sequence Identity:
  • Total samples: 372
  • soil counts: 136
  • aquatic counts: 31
  • animal counts: 53
  • plant counts: 152

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
11607yes, in single cases1Risk group (German classification)
198531Risk group (German classification)
1222161Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium rhodesiae strain CIP 106806 16S ribosomal RNA gene, partial sequenceAF547961540ena36814
20218Mycobacterium rhodesiae 16S rRNA gene, strain DSM 44223TAJ4290471485ena36814

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium rhodesiae strain DSM 4422336814.3wgspatric36814
66792Mycolicibacterium rhodesiae DSM 442232865585367draftimg36814
67770Mycolicibacterium rhodesiae DSM 44223GCA_002086695contigncbi36814
66792Mycolicibacterium rhodesiae DSM 44223GCA_025822805scaffoldncbi36814

GC content

  • @ref: 67770
  • GC-content: 66.6
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno93no
gram-positiveyes89.723no
anaerobicno99.189no
halophileno94.358no
spore-formingno84.411no
glucose-utilyes82.152no
motileno92.105no
flagellatedno97.915no
aerobicyes91.215no
thermophileno99.438yes
glucose-fermentno91.944no

External links

@ref: 11607

culture collection no.: DSM 44223, ATCC 27024, JCM 6363, NCTC 10779, CCUG 37664, CIP 106806

straininfo link

  • @ref: 77864
  • straininfo: 38759

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11607Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44223)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44223
19853Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44223.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
36313Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18976
53792Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37664)https://www.ccug.se/strain?id=37664
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
77864Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38759.1StrainInfo: A central database for resolving microbial strain identifiers
122216Curators of the CIPCollection of Institut Pasteur (CIP 106806)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106806