Strain identifier

BacDive ID: 8412

Type strain: Yes

Species: Mycobacterium duvalii

Strain Designation: 141180001

Strain history: CIP <- 1995, V. Vincent, Inst. Pasteur, Paris, France: strain 14 118 0001 <- ATCC <- NCTC

NCBI tax ID(s): 39688 (species)

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General

@ref: 11619

BacDive-ID: 8412

DSM-Number: 44244

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

description: Mycobacterium duvalii 141180001 is a microaerophile, mesophilic human pathogen that was isolated from cases of leprosy.

NCBI tax id

  • NCBI tax id: 39688
  • Matching level: species

strain history

@refhistory
11619<- A. F. Yassin, C-63 <- NCTC
67770M. Tsukamura 29502 <-- J. L. Stanford 70 <-- NCTC 358 <-- Bayon's old stock in 1920.
118984CIP <- 1995, V. Vincent, Inst. Pasteur, Paris, France: strain 14 118 0001 <- ATCC <- NCTC

doi: 10.13145/bacdive8412.20230509.8.1

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 duvalii
  • full scientific name: Mycobacterium duvalii Stanford and Gunthorpe 1971 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium duvalii

@ref: 11619

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium duvalii

full scientific name: Mycobacterium duvalii Stanford and Gunthorpe 1971

strain designation: 141180001

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.875
69480100positive
118984norod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20030Melon yellow (1028)10-14 days5006
20030Melon yellow (1028)10-14 daysMB7H10
20030Melon yellow (1028)10-14 daysMB7H11
550292-3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11619MYCOBACTERIUM MEDIUM (DSMZ Medium 219)yeshttps://mediadive.dsmz.de/medium/219Name: MYCOBACTERIUM MEDIUM (DSMZ Medium 219) Composition: Agar 20.0 g/l Na2HPO4 x 12 H2O 2.5 g/l Yeast extract 2.0 g/l Proteose peptone no. 3 2.0 g/l Casein peptone 2.0 g/l Sodium citrate 1.5 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.6 g/l Tween 0.5 g/l Glycerol Distilled water
11619MIDDLEBROOK 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
20030MB7H10yesName: 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
20030MB7H11yesName: 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
200305006yesMedium: 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
36324MEDIUM 55 - for Mycobacteriumyes
118984CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
20030positiveoptimum37mesophilic
11619positivegrowth37mesophilic
36324positivegrowth37mesophilic
55029positivegrowth37mesophilic
67770positivegrowth37mesophilic
118984positivegrowth30-37mesophilic
118984nogrowth10psychrophilic
118984nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
55029microaerophile
118984obligate aerobe

spore formation

@refspore formationconfidence
69481no97
69480no99.82

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11898416947citrate-carbon source
118984606565hippurate-hydrolysis
11898417632nitrate+reduction
11898416301nitrite-reduction
118984132112sodium thiosulfate-builds gas from
11898417632nitrate-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: 118984
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 118984
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

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
118984oxidase-
118984beta-galactosidase-3.2.1.23
118984alcohol dehydrogenase-1.1.1.1
118984gelatinase-
118984amylase-
118984caseinase-3.4.21.50
118984catalase+1.11.1.6
118984lipase+
118984lysine decarboxylase-4.1.1.18
118984ornithine decarboxylase-4.1.1.17
118984tryptophan deaminase-
118984urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382acid phosphatase+3.1.3.2
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
20030+-+--+-------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20030-+++++++++----+----
118984-++-+----++---+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118984-+-------------------------------+---------------+----------+-------------------+-------+----------

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
11619cases of leprosy
55029Human case of leprosy
67770Human skin lesion
1189841972

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Microbial#Bacteria
#Host Body-Site#Oral cavity and airways#Airways
#Host Body-Site#Organ#Skin, Nail, Hair

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
11619yes, in single cases1Risk group (German classification)
200301German classification
1189841Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium duvalii 16S ribosomal RNA gene, partial sequenceU947451502ena39688
20218Mycobacterium duvalii strain CIP 104539 16S ribosomal RNA gene, partial sequenceAF547918542ena39688

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium duvalii JCM 6396GCA_010726645completencbi39688
66792Mycolicibacterium duvalii strain JCM 639639688.9completepatric39688
66792Mycolicibacterium duvalii DSM 44244GCA_025823005scaffoldncbi39688

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
motileno94.066no
flagellatedno98.381no
gram-positiveyes91.355no
anaerobicno99.262no
aerobicyes86.328yes
halophileno82.827no
spore-formingno85.744no
glucose-utilyes86.059no
thermophileno98.703yes
glucose-fermentno89.988yes

External links

@ref: 11619

culture collection no.: DSM 44244, ATCC 43910, NCTC 358, CCUG 41352, CIP 104539, JCM 6396, KCTC 9507

straininfo link

  • @ref: 77811
  • straininfo: 45174

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11619Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44244)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44244
20030Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44244.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
36324Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16459
55029Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 41352)https://www.ccug.se/strain?id=41352
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
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
77811Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45174.1StrainInfo: A central database for resolving microbial strain identifiers
118984Curators of the CIPCollection of Institut Pasteur (CIP 104539)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104539