Strain identifier

BacDive ID: 8486

Type strain: Yes

Species: Mycobacterium mageritense

Strain Designation: 938

Strain history: CIP <- 1996, M.J. Garcia, Fac. Med., Madrid, Spain: strain 938 <- CNMVIS, Madrid, Spain: strain 938

NCBI tax ID(s): 1209984 (strain), 53462 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 11802

BacDive-ID: 8486

DSM-Number: 44476

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, human pathogen

description: Mycobacterium mageritense 938 is a facultative anaerobe, mesophilic, Gram-positive human pathogen that was isolated from sputum from asymptomatic human.

NCBI tax id

NCBI tax idMatching level
53462species
1209984strain

strain history

@refhistory
11802<- M. J. Garcia; 938 <- A. Manrique, Centro National de Microbiologica, Madrid
67770CCUG 37984 <-- CIP 104973 <-- M. J. Garcia 938 <-- A. Manrique.
120748CIP <- 1996, M.J. Garcia, Fac. Med., Madrid, Spain: strain 938 <- CNMVIS, Madrid, Spain: strain 938

doi: 10.13145/bacdive8486.20230509.8.1

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 mageritense
  • full scientific name: Mycobacterium mageritense Domenech et al. 1997

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium mageritense

@ref: 11802

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium mageritense

full scientific name: Mycobacterium mageritense Domenech et al. 1997 emend. Nouioui et al. 2018

strain designation: 938

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120748rod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19865Ivory10-14 days5006
19865Ivory10-14 daysMB7H10
19865Ivory10-14 daysMB7H11

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11802MIDDLEBROOK 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
11802LÖWENSTEIN-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
19865MB7H10yesName: 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
19865MB7H11yesName: 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
198655006yesMedium: 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
36361MEDIUM 55 - for Mycobacteriumyes
120748CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
19865positiveoptimum37mesophilic
11802positivegrowth37mesophilic
36361positivegrowth37mesophilic
67770positivegrowth37mesophilic
120748positivegrowth22-37
120748nogrowth10psychrophilic
120748nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120748
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no95
69480no98.936

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
120748606565hippurate-hydrolysis
12074817632nitrate+reduction
12074816301nitrite-reduction
12074817632nitrate-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: 120748
  • 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
120748oxidase-
120748beta-galactosidase-3.2.1.23
120748gelatinase-
120748catalase+1.11.1.6
120748gamma-glutamyltransferase+2.3.2.2
120748urease+3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
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
19865--+-----++-----+-+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19865-++-+-+++------+---
120748++++++++-++---++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120748++++++----------++-----+--+++--+++--++--+-------++++----+---+------+--++++++-++++--++-+++-+++++-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
11802sputum from asymptomatic humanMadrid, Cantoblanco HospitalSpainESPEurope
53998Human sputumMadridSpainESPEurope1987
67770Sputum of asymptomatic humanSpainESPEurope
120748Human, SputumMadridSpainESPEurope1987

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Sputum

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
11802yesyes2Risk group (German classification)
198651Risk group (German classification)
1207481Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218M.mageritense 16S rRNA geneX99838634ena1209984
20218Mycobacterium mageritense strain CIP 104973 16S ribosomal RNA gene, partial sequenceAF547944540ena1209984
20218Mycobacterium mageritense strain CIP 104973 16S ribosomal RNA gene, partial sequenceAY4570761485ena53462
20218Mycobacterium mageritense 16S rRNA gene, type strain DSM 44476AJ6993991497ena1209984

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium mageritense JCM 12375GCA_010727475completencbi53462
66792Mycobacterium mageritense DSM 444761209984.3wgspatric1209984
66792Mycolicibacterium mageritense strain JCM 1237553462.6completepatric53462
66792Mycolicibacterium mageritense DSM 444762617271075draftimg1209984
67770Mycolicibacterium mageritense DSM 44476 = CIP 104973GCA_000612825contigncbi1209984

GC content

@refGC-contentmethod
6777066.9genome sequence analysis
6777066high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
motileno91.962no
flagellatedno97.922no
gram-positiveyes84.674no
anaerobicno98.829no
aerobicyes88.173no
halophileno93.984no
spore-formingno74.376no
thermophileno99.536yes
glucose-utilyes89.814no
glucose-fermentno89.371yes

External links

@ref: 11802

culture collection no.: DSM 44476, ATCC 700351, CIP 104973, CCUG 37984, JCM 12375

straininfo link

  • @ref: 77880
  • straininfo: 43888

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics24786954Draft Genome Sequence of Mycobacterium mageritense DSM 44476T.Croce O, Robert C, Raoult D, Drancourt MGenome Announc10.1128/genomeA.00354-142014
Phylogeny30696899Genome-guided and mass spectrometry investigation of natural products produced by a potential new actinobacterial strain isolated from a mangrove ecosystem in Futian, Shenzhen, China.Hu D, Gao C, Sun C, Jin T, Fan G, Mok KM, Lee SMSci Rep10.1038/s41598-018-37475-w2019Anti-Bacterial Agents/isolation & purification/metabolism/*pharmacology, Bacterial Typing Techniques, Biological Products/isolation & purification/metabolism/*pharmacology, China, DNA, Bacterial/genetics, Genome, Bacterial/*genetics, Mycobacterium/classification/*genetics/isolation & purification/*metabolism, RNA, Ribosomal, 16S/genetics, Secondary Metabolism/physiology, Sequence Analysis, DNA, Soil Microbiology, Wetlands, Whole Genome SequencingMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11802Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44476)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44476
19865Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44476.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
36361Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16940
53998Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37984)https://www.ccug.se/strain?id=37984
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
77880Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43888.1StrainInfo: A central database for resolving microbial strain identifiers
120748Curators of the CIPCollection of Institut Pasteur (CIP 104973)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104973