Strain identifier

BacDive ID: 8403

Type strain: Yes

Species: Mycobacterium intracellulare

Strain Designation: 3600, 140310001

Strain history: CIP <- 1994, V. Vincent, Inst. Pasteur, Paris, France: strain 14 031 0001 <- 1966, ATCC <- R.E. Gordon <- D. Smith (Cuttino and McCabe's original strain)

NCBI tax ID(s): 1767 (species)

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General

@ref: 10880

BacDive-ID: 8403

DSM-Number: 43223

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

description: Mycobacterium intracellulare 3600 is a microaerophile, mesophilic human pathogen that was isolated from Human lymph node.

NCBI tax id

  • NCBI tax id: 1767
  • Matching level: species

strain history

@refhistory
10880<- I. Tarnok, SN 424 <- ATCC <- R.E. Gordon, 3600 <- D. Smith
67770M. Tsukamura 13085 <-- ATCC 13950 <-- R. E. Gordon 3600 <-- D. Smith (J. T. Cuttino and A. M. McCabe's original strain).
120272CIP <- 1994, V. Vincent, Inst. Pasteur, Paris, France: strain 14 031 0001 <- 1966, ATCC <- R.E. Gordon <- D. Smith (Cuttino and McCabe's original strain)

doi: 10.13145/bacdive8403.20230509.8.1

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 intracellulare
  • full scientific name: Mycobacterium intracellulare corrig. (Cuttino and McCabe 1949) Runyon 1965 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Mycobacterium intracellularis
    20215Mycobacterium paraintracellulare
    20215Nocardia intracellularis

@ref: 10880

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium intracellulare subsp. intracellulare

full scientific name: Mycobacterium intracellulare subsp. intracellulare (Cuttino and McCabe 1949) Castejon et al. 2018

strain designation: 3600, 140310001

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.229
69480100positive
120272norod-shaped

colony morphology

  • @ref: 49062
  • incubation period: 6 days

multimedia

  • @ref: 10880
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43223.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10880MIDDLEBROOK 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
120272CIP Medium 267yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=267

culture temp

@refgrowthtypetemperaturerange
10880positivegrowth37mesophilic
67770positivegrowth37mesophilic
120272positivegrowth22-45
120272nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
49062microaerophile
120272obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.956

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
120272606565hippurate-hydrolysis
12027217632nitrate+reduction
12027216301nitrite-reduction
12027217632nitrate-respiration

metabolite production

  • @ref: 120272
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
120272oxidase-
120272beta-galactosidase-3.2.1.23
120272gelatinase-
120272catalase-1.11.1.6
120272gamma-glutamyltransferase-2.3.2.2
120272urease-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
68382valine arylamidase-
68382cystine arylamidase+3.4.11.3
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 zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120272-+++-+-++-++----+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
67770Human lymph node
120272North CarolinaUnited States of AmericaUSANorth America1949

taxonmaps

  • @ref: 69479
  • File name: preview.99_402.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_37;97_39;98_43;99_402&stattab=map
  • Last taxonomy: Mycobacterium
  • 16S sequence: JF271818
  • Sequence Identity:
  • Total samples: 24078
  • soil counts: 12779
  • aquatic counts: 4789
  • animal counts: 3677
  • plant counts: 2833

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
10880yesyes2Risk group (German classification)
1202722Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium intracellulare strain ATCC13950 16S ribosomal RNA (rrs) gene, partial sequenceAF059849173ena487521
20218Mycobacterium intracellulare ATCC 13950 16S ribosomal RNA gene, partial sequenceGQ1532761495ena487521
20218Mycobacterium intracellulare ATCC 13950 16S ribosomal RNA gene, partial sequenceJF2718181395ena487521
20218Mycobacterium intracellulare ATCC 13950 16S-23S ribosomal RNA intergenic spacer, partial sequenceJQ411532280ena487521
20218Mycobacterium intracellulare sequevar Min-A partial 16S ribosomal RNA gene, partial 23S ribosomal RNA gene, and complete internal transcribed spacerL07859309ena1767
20218Mycobacterium intracellulare strain ATCC 15985 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequenceEF521903438ena1767
20218M.intracellulare 16S ribosomal RNA geneM59276146ena1767
20218Mycobacterium intracellulare 16S rRNA geneX529271452ena1767
20218Mycobacterium intracellulare CCUG:28005 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceHM584723183ena1767
20218Mycobacterium intracellulare strain CIP 104243 16S ribosomal RNA gene, partial sequenceAF547939554ena1767
20218Mycobacterium intracellulare 16S rRNA geneAJ5360361440ena1767
20218Mycobacterium intracellulare DNA for 16S rRNA, internal transcribed spacer, 23S rRNAAB026691438ena1767
20218M.intracellulare 16S-23S rDNA internal transcribed spacerX74057279ena1767
20218M.intracellulare leader region of 16S rRNA geneX74063191ena1767

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium intracellulare ATCC 13950GCA_000277125completencbi487521
66792Mycobacterium intracellulare ATCC 13950487521.5wgspatric487521
66792Mycobacterium intracellulare ATCC 13950487521.10completepatric487521
66792Mycobacterium intracellulare ATCC 139502519103109completeimg487521
66792Mycobacterium intracellulare ATCC 13950645058739draftimg487521
67770Mycobacterium intracellulare ATCC 13950GCA_000172115contigncbi487521
66792Mycobacterium intracellulare ATCC 13950GCA_023278525completencbi487521

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.021no
flagellatedno99.04no
gram-positiveyes91.375no
anaerobicno99.568yes
aerobicyes90.403yes
halophileno91.058no
spore-formingno85.754no
thermophileno98.129yes
glucose-utilyes65.229no
glucose-fermentno91.099no

External links

@ref: 10880

culture collection no.: DSM 43223, ATCC 13950, ATCC 15985, JCM 6384, NCTC 10682, CCUG 28005, NCTC 13025, TMC 1406, CIP 104243, SN 424, KCTC 9514

straininfo link

  • @ref: 77802
  • straininfo: 92812

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity3394452Further studies on colistin (polymyxin E)-induced cell leakage in mycobacteria: Mg++ efflux in Mycobacterium avium and its effects on drug-susceptibility.Rastogi N, Potar MC, Henrotte JG, Franck G, David HLZentralbl Bakteriol Mikrobiol Hyg A10.1016/s0176-6724(88)80010-51988Amoxicillin/pharmacology, Carbenicillin/pharmacology, Clavulanic Acid, Clavulanic Acids/pharmacology, Colistin/*pharmacology, Kinetics, Magnesium/*metabolism, Mycobacterium avium/*drug effects/growth & development/metabolismEnzymology
Enzymology8250904Cloning, sequencing and expression of the gene for alpha antigen from Mycobacterium intracellulare and use of PCR for the rapid identification of Mycobacterium intracellulare.Kitaura H, Ohara N, Matsuo T, Tasaka H, Kobayashi K, Yamada TBiochem Biophys Res Commun10.1006/bbrc.1993.24171993Amino Acid Sequence, Animals, Antigens, Bacterial/analysis/*genetics, Base Sequence, Cloning, Molecular, DNA Primers, DNA, Bacterial/*analysis/genetics, Escherichia coli, Gene Expression, *Genes, Bacterial, Humans, Molecular Sequence Data, Molecular Weight, Mycobacterium/genetics, Mycobacterium avium Complex/*genetics/immunology/*isolation & purification, Polymerase Chain Reaction/methods, Restriction Mapping, Sequence Homology, Amino AcidPathogenicity
Pathogenicity15780634Antitubercular agents. Part 1: synthesis of phthalimido- and naphthalimido-linked phenazines as new prototype antitubercular agents.Kamal A, Hari Babu A, Venkata Ramana A, Sinha R, Yadav JS, Arora SKBioorg Med Chem Lett10.1016/j.bmcl.2005.01.0852005Antitubercular Agents/*chemical synthesis/pharmacology, Imides/*chemistry, Microbial Sensitivity Tests, Mycobacterium avium/drug effects, Mycobacterium avium Complex/drug effects, Mycobacterium tuberculosis/drug effects, Naphthalenes/*chemistry, Phenazines/*chemical synthesis/pharmacology, Phthalimides/chemistry, Structure-Activity Relationship
Phylogeny20350295Variable-number tandem-repeat markers for typing Mycobacterium intracellulare strains isolated in humans.Dauchy FA, Degrange S, Charron A, Dupon M, Xin Y, Bebear C, Maugein JBMC Microbiol10.1186/1471-2180-10-932010Adolescent, Adult, Aged, Aged, 80 and over, Carrier State/microbiology, Child, Child, Preschool, Cluster Analysis, DNA, Bacterial/chemistry, Female, Humans, *Interspersed Repetitive Sequences, Male, Middle Aged, *Minisatellite Repeats, Mycobacterium avium Complex/classification/*genetics, Mycobacterium avium-intracellulare Infection/*microbiology, Phylogeny, Polymerase Chain Reaction/*methodsPathogenicity
Phylogeny22427442Mycobacterium yongonense sp. nov., a slow-growing non-chromogenic species closely related to Mycobacterium intracellulare.Kim BJ, Math RK, Jeon CO, Yu HK, Park YG, Kook YH, Kim BJInt J Syst Evol Microbiol10.1099/ijs.0.037465-02012DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Genes, Bacterial, Humans, Lipids/analysis, Lung Diseases/*microbiology, Molecular Sequence Data, Mycobacterium/*classification/genetics/isolation & purification, Mycobacterium Infections/*microbiology, Mycobacterium avium Complex/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of KoreaPathogenicity
Genetics22535933Complete genome sequence of Mycobacterium intracellulare strain ATCC 13950(T).Kim BJ, Choi BS, Lim JS, Choi IY, Lee JH, Chun J, Kook YH, Kim BJJ Bacteriol10.1128/JB.00295-122012*Genome, Bacterial, Humans, Molecular Sequence Data, Mycobacterium avium Complex/*geneticsPathogenicity
Genetics25370496Comparative analyses of nonpathogenic, opportunistic, and totally pathogenic mycobacteria reveal genomic and biochemical variabilities and highlight the survival attributes of Mycobacterium tuberculosis.Rahman SA, Singh Y, Kohli S, Ahmad J, Ehtesham NZ, Tyagi AK, Hasnain SEmBio10.1128/mBio.02020-142014*Adaptation, Biological, *Adaptation, Physiological, Bacterial Proteins/genetics, Cluster Analysis, *Environmental Microbiology, Evolution, Molecular, *Genetic Variation, Genome, Bacterial, Humans, Metabolic Networks and Pathways/*genetics, Mycobacterium/*genetics/metabolism/pathogenicity, Phylogeny, Sequence Homology, Amino Acid, Tuberculosis/*microbiologyPathogenicity
Genetics27031100Molecular Taxonomic Evidence for Two Distinct Genotypes of Mycobacterium yongonense via Genome-Based Phylogenetic Analysis.Kim BJ, Kim BR, Lee SY, Kim GN, Kook YH, Kim BJPLoS One10.1371/journal.pone.01527032016Bacterial Proteins/*genetics, *Genome, Bacterial, *Genotype, Mycobacterium/*genetics, *Phylogeny, Species SpecificityPhylogeny
Phylogeny27189351Mycobacterium paraintracellulare sp. nov., for the genotype INT-1 of Mycobacterium intracellulare.Lee SY, Kim BJ, Kim H, Won YS, Jeon CO, Jeong J, Lee SH, Lim JH, Lee SH, Kim CK, Kook YH, Kim BJInt J Syst Evol Microbiol10.1099/ijsem.0.0011582016Aged, Aged, 80 and over, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Female, Genes, Bacterial, Humans, Male, Middle Aged, Multilocus Sequence Typing, Mycobacterium Infections/microbiology, Mycobacterium avium Complex/*classification/genetics/isolation & purification, Mycolic Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sputum/*microbiologyPathogenicity
Genetics29702266Genome sequence of Mycobacterium yongonense RT 955-2015 isolate from a patient misdiagnosed with multidrug-resistant tuberculosis: First clinical detection in Tanzania.Mnyambwa NP, Kim DJ, Ngadaya E, Chun J, Ha SM, Petrucka P, Addo KK, Kazwala RR, Mfinanga SGInt J Infect Dis10.1016/j.ijid.2018.04.7962018Diagnostic Errors, Genotype, Humans, Male, Middle Aged, Mycobacterium avium Complex/classification/genetics/*isolation & purification, Phylogeny, Tanzania, Tuberculosis, Multidrug-Resistant/diagnosis/*microbiology, Whole Genome SequencingPhylogeny
Phylogeny30231956A definition of the Mycobacterium avium complex for taxonomical and clinical purposes, a review.van Ingen J, Turenne CY, Tortoli E, Wallace RJ Jr, Brown-Elliott BAInt J Syst Evol Microbiol10.1099/ijsem.0.0030262018Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Mycobacterium avium Complex/*classification, Nontuberculous Mycobacteria/*classification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Genetics32214196Genome-wide identification of essential genes in Mycobacterium intracellulare by transposon sequencing - Implication for metabolic remodeling.Tateishi Y, Minato Y, Baughn AD, Ohnishi H, Nishiyama A, Ozeki Y, Matsumoto SSci Rep10.1038/s41598-020-62287-22020DNA Transposable Elements/*genetics, DNA, Bacterial/*genetics, Drug Discovery, Genome, Bacterial/*genetics, Genomics/*methods, Gluconeogenesis/genetics, Glyoxylates/metabolism, Humans, Mycobacterium Infections, Nontuberculous/microbiology, Mycobacterium avium Complex/*genetics/growth & development/*metabolism/pathogenicity, Proteasome Endopeptidase Complex/genetics, Sequence Analysis, DNA/*methods, Succinic Acid/metabolism, Virulence/geneticsMetabolism
32751435Feature of Adhesins Produced by Human Clinical Isolates of Mycobacterium intracellulare, Mycobacterium intracellulare subsp. chimaera and Closely Related Species.Lefrancois LH, Cochard T, Branger M, Peuchant O, Conde C, Pastuszka A, Locht C, Lanotte P, Biet FMicroorganisms10.3390/microorganisms80811542020
Phylogeny33823816Comparative genomic analysis of Mycobacterium intracellulare: implications for clinical taxonomic classification in pulmonary Mycobacterium avium-intracellulare complex disease.Tateishi Y, Ozeki Y, Nishiyama A, Miki M, Maekura R, Fukushima Y, Nakajima C, Suzuki Y, Matsumoto SBMC Microbiol10.1186/s12866-021-02163-92021Genes, Bacterial/genetics, Genetic Variation, *Genome, Bacterial/genetics, Genomics, Humans, *Mycobacterium avium Complex/classification/genetics/pathogenicity, *Mycobacterium avium-intracellulare Infection/microbiology, *Phylogeny, Plasmids/genetics, Virulence/geneticsGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10880Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43223)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43223
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
49062Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28005)https://www.ccug.se/strain?id=28005
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/
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
77802Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92812.1StrainInfo: A central database for resolving microbial strain identifiers
120272Curators of the CIPCollection of Institut Pasteur (CIP 104243)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104243