Strain identifier

BacDive ID: 8429

Type strain: Yes

Species: Mycobacterium simiae

Strain Designation: 14 102 0001, N29, 3015

Strain history: CIP <- 1995, V. Vincent, Inst. Pasteur, Paris, France: strain 14 102 0001 <- ATCC <- E. Runyon: strain 3015 <- J. Weiszfeiler: strain N29

NCBI tax ID(s): 1236483 (strain), 1784 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 11563

BacDive-ID: 8429

DSM-Number: 44165

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

description: Mycobacterium simiae 14 102 0001 is an obligate aerobe, mesophilic human pathogen that was isolated from Indian monkey .

NCBI tax id

NCBI tax idMatching level
1784species
1236483strain

strain history

@refhistory
11563<- ATCC <- E. Runyon, 3015 <- J. Weiszfeiler, N 29
67770CCUG 29114 <-- M. Ridell <-- A. Lind <-- ATCC 25275 <-- E. H. Runyon 3015 <-- J. Weiszfeiler N29.
122614CIP <- 1995, V. Vincent, Inst. Pasteur, Paris, France: strain 14 102 0001 <- ATCC <- E. Runyon: strain 3015 <- J. Weiszfeiler: strain N29

doi: 10.13145/bacdive8429.20230509.8.1

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 simiae
  • full scientific name: Mycobacterium simiae Karassova et al. 1965 (Approved Lists 1980)

@ref: 11563

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium simiae

full scientific name: Mycobacterium simiae Karassova et al. 1965 emend. Nouioui et al. 2018

strain designation: 14 102 0001, N29, 3015

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no96.185
69480100positive
122614nooval-shaped

colony morphology

@refincubation periodmedium usedcolony color
1984510-14 days5006
1984510-14 daysMB7H10Daffodil yellow
1984510-14 daysMB7H11Daffodil yellow

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11563MYCOBACTERIUM 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
11563MIDDLEBROOK 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
19845MB7H10yesName: 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
19845MB7H11yesName: 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
198455006yesMedium: 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
36246MEDIUM 55 - for Mycobacteriumyes
122614CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
19845positiveoptimum37mesophilic
11563positivegrowth37mesophilic
36246positivegrowth37mesophilic
67770positivegrowth37mesophilic
122614positivegrowth30-37mesophilic
122614nogrowth10psychrophilic
122614nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122614
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no94
69480no99.966

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1226144853esculin-hydrolysis
122614606565hippurate+hydrolysis
12261417632nitrate+reduction
12261416301nitrite-reduction
12261417632nitrate-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: 122614
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 122614
  • 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
122614oxidase-
122614beta-galactosidase-3.2.1.23
122614alcohol dehydrogenase-1.1.1.1
122614gelatinase-
122614catalase+1.11.1.6
122614tween esterase-
122614lysine decarboxylase-4.1.1.18
122614ornithine decarboxylase-4.1.1.17
122614urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
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
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
19845-+-----------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19845-+++++---++--------
122614-++-+-+--++---------

Isolation, sampling and environmental information

isolation

@refsample typehost species
11563Indian monkey (Macaca mulatta)Macaca mulatta
67770Indian monkey (Macaca mulatta)Macaca mulatta
122614Indian monkey

isolation source categories

  • Cat1: #Host
  • Cat2: #Mammals
  • Cat3: #Primates

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
11563yesyes2Risk group (German classification)
198452Risk group (German classification)
1226142Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium simiae DNA, 16S-23S ribosomal RNA intergenic spacer, strain: ATCC 25275AB547405281ena1784
20218Mycobacterium simiae gene for 16S ribosomal RNA, partial cds, strain: ATCC 25275AB5474061471ena1784
20218Mycobacterium simiae partial 16S rRNA gene, strain ATCC 25275AJ439538644ena1784
20218M.simiae 16S ribosomal RNA geneM59269145ena1784
20218Mycobacterium simiae 16S rRNA geneX529311484ena1784
20218Mycobacterium simiae strain CIP 104531 16S ribosomal RNA gene, partial sequenceAF547966542ena1784
20218Mycobacterium simiae DNA for 16S rRNA, internal transcribed spacer, 23S rRNAAB026694440ena1784
11563Mycobacterium simiae strain ATCC 25275 16S ribosomal RNA gene, partial sequenceGQ1532801483ena1784

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium simiae JCM 12377GCA_010727605completencbi1784
66792Mycobacterium simiae ATCC 25275 = DSM 441651236483.3wgspatric1236483
66792Mycobacterium simiae strain JCM 123771784.27completepatric1784
66792Mycobacterium simiae ATCC 252752600254956draftimg1236483
67770Mycobacterium simiae ATCC 25275 = DSM 44165GCA_000455305scaffoldncbi1236483

GC content

@refGC-contentmethod
6777065.15genome sequence analysis
6777066.2genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
motileno93.203no
flagellatedno98.613no
gram-positiveyes89.396no
anaerobicno99.051no
aerobicyes92.861no
halophileno95.512no
spore-formingno87.84no
glucose-utilyes71.401no
thermophileno97.767yes
glucose-fermentno92.988yes

External links

@ref: 11563

culture collection no.: DSM 44165, ATCC 25275, TMC 1226, JCM 12377, CCUG 29114, CCUG 42427, CIP 104531

straininfo link

  • @ref: 77828
  • straininfo: 38461

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9611792Analysis of lipids reveals differences between 'Mycobacterium habana' and Mycobacterium simiae.Mederos LM, Valdivia JA, Sempere MA, Valero-Guillen PLMicrobiology (Reading)10.1099/00221287-144-5-11811998Bacterial Typing Techniques, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, Fatty Acids/*analysis, Glycolipids/*analysis, Mycolic Acids/analysis, Nontuberculous Mycobacteria/*chemistry/*classification, Species Specificity
Phylogeny18397261New variants of polar glycopeptidolipids detected in Mycobacterium simiae, including 'habana' strains, as evidenced by electrospray ionization-ion trap-mass spectrometry.Mederos L, Valdivia JA, Valero-Guillen PLJ Appl Microbiol10.1111/j.1365-2672.2008.03796.x2008Bacteriological Techniques, Glycolipids/*analysis, Nontuberculous Mycobacteria/*chemistry, Species Specificity, Spectrometry, Mass, Electrospray Ionization, Tuberculosis/*microbiology
Phylogeny20639227Mycobacterium sherrisii sp. nov., a slow-growing non-chromogenic species.van Ingen J, Tortoli E, Selvarangan R, Coyle MB, Crump JA, Morrissey AB, Dekhuijzen PNR, Boeree MJ, van Soolingen DInt J Syst Evol Microbiol10.1099/ijs.0.024752-02010Africa, Bacterial Proteins/genetics, Bacterial Typing Techniques, Cell Wall/chemistry, Chaperonin 60/genetics, Chromatography, High Pressure Liquid, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA, Ribosomal Spacer/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Enzyme Stability, Enzymes/metabolism, Hot Temperature, Humans, Molecular Sequence Data, Mycobacterium/*classification/genetics/growth & development/*isolation & purification, Mycolic Acids/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Time FactorsEnzymology
Pathogenicity20688816Structural studies of cord factors from Mycobacterium simiae related to the capacity for tumour necrosis factor alpha (alpha-TNF) induction.Mederos LM, Montoro EH, Bernabeu A, Linares C, Valero-Guillen PLMicrobiology (Reading)10.1099/mic.0.042077-02010Animals, Cell Line, Cord Factors/*chemistry/genetics/*immunology, Humans, Mice, Molecular Structure, Mycobacterium/chemistry/genetics/*immunology, Tuberculosis/*immunology/microbiology, Tumor Necrosis Factor-alpha/*immunology
Genetics23991261Non-contiguous genome sequence of Mycobacterium simiae strain DSM 44165(T.).Sassi M, Robert C, Raoult D, Drancourt MStand Genomic Sci10.4056/sigs.37073492013

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11563Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44165)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44165
19845Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44165.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
36246Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16450
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
77828Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38461.1StrainInfo: A central database for resolving microbial strain identifiers
122614Curators of the CIPCollection of Institut Pasteur (CIP 104531)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104531