Strain identifier

BacDive ID: 8219

Type strain: Yes

Species: Mycobacterium chitae

Strain Designation: 2502, 14 116 0001

Strain history: CIP <- 1998, V. Vincent, Inst. Pasteur, Paris, France: strain 14 116 0001 <- ATCC <- M. Tsukamura: strain 2502

NCBI tax ID(s): 1792 (species)

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General

@ref: 11942

BacDive-ID: 8219

DSM-Number: 44633

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive

description: Mycobacterium chitae 2502 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1792
  • Matching level: species

strain history

@refhistory
11942<- ATCC <- M. Tsukamura
67770CIP 105383 <-- V. Vincent <-- ATCC 19627 <-- M. Tsukamura 2502.
118235CIP <- 1998, V. Vincent, Inst. Pasteur, Paris, France: strain 14 116 0001 <- ATCC <- M. Tsukamura: strain 2502

doi: 10.13145/bacdive8219.20230509.8.1

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 chitae
  • full scientific name: Mycobacterium chitae Tsukamura 1967 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium chitae

@ref: 11942

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium chitae

full scientific name: Mycobacterium chitae Tsukamura 1967

strain designation: 2502, 14 116 0001

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
118235rod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19871Cream10-14 days5006
19871Cream10-14 daysBUG
19871Cream10-14 daysMB7H9

multimedia

  • @ref: 11942
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44633.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11942LÖWENSTEIN-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
11942MIDDLEBROOK 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
19871BUGyes
198715006yesMedium: 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
19871MB7H9yesName: Middlebrook 7H9 (MB7H9) Broth Base Composition: Middelbrook 7H9 Broth Base 4.7 g/l Glycerol 2.0 g/l Casaminoacids 11.0 g/l Yeast extract 5.5 g/l Tween80 (20%) 2.5 g/l OADC-Enrichment 100 ml Agar 15.0 g/l Preparation: Dissolve in Milli-Q-H2O. Before Use add 10% OADC stock solution Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Maintenance and revitalization Organisms: 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
32690MEDIUM 55 - for Mycobacteriumyes
118235CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
19871positiveoptimum37mesophilic
11942positivegrowth37mesophilic
32690positivegrowth37mesophilic
54825positivegrowth37mesophilic
67770positivegrowth37mesophilic
118235positivegrowth22-37
118235nogrowth10psychrophilic
118235nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
54825microaerophile
118235obligate aerobe

spore formation

@refspore formationconfidence
69481no98
69480no99.874

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
118235hippurate-hydrolysis606565
118235nitrate+reduction17632
118235nitrite-reduction16301
118235nitrate-respiration17632
68379nitrate-reduction17632
68379esculin-hydrolysis4853
68379urea+hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose+fermentation17992
68379glycogen-fermentation28087

metabolite production

  • @ref: 118235
  • 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
118235oxidase-
118235beta-galactosidase+3.2.1.23
118235gelatinase-
118235amylase-
118235DNase-
118235caseinase-3.4.21.50
118235catalase+1.11.1.6
118235tween esterase-
118235lecithinase-
118235lipase-
118235protease-
118235tryptophan deaminase-
118235urease+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
68382alpha-chymotrypsin-3.4.21.1
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
19871----+----+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19871-++-++++-+---+-----
118235-++-+----++--+------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118235-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118235++-+---------------------------+++--------------------------+------+-------+--------------------+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11942soilJapanJPNAsia
67770Soil (after injection to hen)
118235Environment, SoilJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119421Risk group (German classification)
198711Risk group (German classification)
1182351Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218M.chitae 16S ribosomal RNAM295601359ena1792
20218M.chitae 16S ribosomal RNA, partX556031457ena1792
20218M.chitae 16S rRNAX678741437ena1792
20218Mycobacterium chitae strain CIP 105383 16S ribosomal RNA gene, partial sequenceAF547910540ena1792

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium chitae NCTC10485GCA_900637205completencbi1792
66792Mycolicibacterium chitae JCM 12403GCA_010727725completencbi1792
66792Mycolicibacterium chitae strain JCM 124031792.9completepatric1792
66792Mycolicibacterium chitae strain NCTC104851792.7completepatric1792
66792Mycolicibacterium chitae NCTC 104852867052265completeimg1792
66792Mycolicibacterium chitae DSM 44633GCA_025821725scaffoldncbi1792

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
flagellatedno98.35no
gram-positiveyes84.567no
anaerobicno99.008yes
aerobicyes85.794no
halophileno88.848no
spore-formingno87.577no
thermophileno98.721no
glucose-utilyes86.738no
motileno93.407no
glucose-fermentno90.768no

External links

@ref: 11942

culture collection no.: DSM 44633, ATCC 19627, CIP 105383, CCUG 39504, NCTC 10485, JCM 12403

straininfo link

  • @ref: 77622
  • straininfo: 37040

literature

  • topic: Enzymology
  • Pubmed-ID: 15722145
  • title: Multicenter evaluation of mycobacteria identification by PCR restriction enzyme analysis in laboratories from Latin America and the Caribbean.
  • authors: Leao SC, Bernardelli A, Cataldi A, Zumarraga M, Robledo J, Realpe T, Mejia GI, da Silva Telles MA, Chimara E, Velazco M, Fernandez J, Rodrigues PA, Guerrero MI, Leon CI, Porras TB, Rastogi N, Goh KS, Suffys P, da Silva Rocha A, dos Santos Netto D, Ritacco V, Lopez B, Barrera L, Palomino JC, Martin A, Portaels F
  • journal: J Microbiol Methods
  • DOI: 10.1016/j.mimet.2004.11.015
  • year: 2004
  • mesh: Bacterial Proteins/chemistry/genetics, Chaperonin 60, Chaperonins/chemistry/genetics, DNA, Bacterial/chemistry/genetics, Guadeloupe, Humans, Mycobacterium/genetics/*isolation & purification, Mycobacterium Infections/*diagnosis, Polymerase Chain Reaction/*methods/standards, Restriction Mapping, South America
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11942Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44633)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44633
19871Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44633.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
32690Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17396
54825Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39504)https://www.ccug.se/strain?id=39504
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/
68371Automatically annotated from API 50CH acid
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
77622Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID37040.1StrainInfo: A central database for resolving microbial strain identifiers
118235Curators of the CIPCollection of Institut Pasteur (CIP 105383)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105383