Strain identifier

BacDive ID: 8370

Type strain: Yes

Species: Mycobacterium xenopi

Strain Designation: 1482, 14 035 0001

Strain history: CIP <- 1994, V. Vincent, Inst. Pasteur, Paris, France: strain 14 035 0001 <- ATCC <- TMC: strain 1482 <- NCTC <- H. Schwabacher

NCBI tax ID(s): 1789 (species)

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General

@ref: 11444

BacDive-ID: 8370

DSM-Number: 43995

keywords: genome sequence, 16S sequence, Bacteria, thermophilic, rod-shaped, human pathogen

description: Mycobacterium xenopi 1482 is a thermophilic, rod-shaped human pathogen that was isolated from adult female toad, Xenopus laevis.

NCBI tax id

  • NCBI tax id: 1789
  • Matching level: species

strain history

@refhistory
11444<- ATCC <- TMC <- NCTC <- H. Schwabacher
67770CIP 104035 <-- V. Vincent <-- ATCC 19250 <-- TMC 1482 <-- NCTC 10042 <-- H. Schwabacher.
123974CIP <- 1994, V. Vincent, Inst. Pasteur, Paris, France: strain 14 035 0001 <- ATCC <- TMC: strain 1482 <- NCTC <- H. Schwabacher

doi: 10.13145/bacdive8370.20230509.8.1

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 xenopi
  • full scientific name: Mycobacterium xenopi corrig. Schwabacher 1959 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Mycobacterium xenopei

@ref: 11444

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium xenopi

full scientific name: Mycobacterium xenopi Schwabacher 1959 emend. Nouioui et al. 2018

strain designation: 1482, 14 035 0001

type strain: yes

Morphology

cell morphology

  • @ref: 123974
  • cell shape: rod-shaped
  • motility: no

multimedia

  • @ref: 11444
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43995.jpg
  • caption: Medium 645 45°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11444MIDDLEBROOK 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
11444LÖWENSTEIN-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
34458MEDIUM 55 - for Mycobacteriumyes
123974CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
11444positivegrowth45thermophilic
34458positivegrowth37mesophilic
67770positivegrowth37mesophilic
123974positivegrowth30-45
123974nogrowth10psychrophilic
123974nogrowth22psychrophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
123974606565hippurate-hydrolysis
12397417632nitrate-reduction
12397416301nitrite-reduction

metabolite production

  • @ref: 123974
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
123974oxidase-
123974beta-galactosidase+3.2.1.23
123974gelatinase-
123974catalase-1.11.1.6
123974gamma-glutamyltransferase-2.3.2.2
123974urease-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
123974--++-+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typehost species
11444adult female toad, Xenopus laevisXenopus laevis
67770Adult female toad, Xenopus laevisXenopus laevis
123974Adult female toad, Xenopus larvis

isolation source categories

  • Cat1: #Host
  • Cat2: #Amphibia

taxonmaps

  • @ref: 69479
  • File name: preview.99_2388.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_475;97_543;98_1860;99_2388&stattab=map
  • Last taxonomy: Mycobacterium xenopi subclade
  • 16S sequence: X52929
  • Sequence Identity:
  • Total samples: 6376
  • soil counts: 795
  • aquatic counts: 566
  • animal counts: 4741
  • plant counts: 274

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
11444yesyes2Risk group (German classification)
1239742Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium xenopi strain ATCC19250 16S ribosomal RNA (rrs) gene, partial sequenceAF059844179ena1789
20218Mycobacterium xenopi strain ATCC 19250 16S-23S ribosomal RNA intergenic spacer, partial sequenceHQ293150132ena1789
20218Mycobacterium xenopi strain ATCC 19250 16S ribosomal RNA gene, partial sequenceJQ348120216ena1789
20218Mycobacterium xenopi 16S ribosomal RNA and 23S ribosomal RNA gene fragmentsL15624397ena1789
20218M.xenopi 16S ribosomal RNA geneM59272151ena1789
20218M.xenopi 16S ribosomal rRNAM616641376ena1789
20218Mycobacterium xenopi 16S rRNA geneX529291474ena1789
20218Mycobacterium xenopi partial 16S rRNAX538951225ena1789
20218Mycobacterium xenopi strain CIP 104035 16S ribosomal RNA gene, partial sequenceAF547982560ena1789
20218Mycobacterium xenopi 16S rRNA geneAJ5360331480ena1789

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium xenopi strain DSM 439951789.6wgspatric1789
66792Mycobacterium xenopi strain JCM 15661T1789.10completepatric1789
66792Mycobacterium xenopi strain NCTC100421789.9wgspatric1789
66792Mycobacterium xenopi NCTC 100422811995252draftimg1789
67770Mycobacterium xenopi DSM 43995GCA_002102015contigncbi1789
67770Mycobacterium xenopi NCTC10042GCA_900453395contigncbi1789
66792Mycobacterium xenopi JCM 15661GCA_009936235completencbi1789

GC content

  • @ref: 67770
  • GC-content: 65.9
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.375no
gram-positiveyes85.296no
anaerobicno98.384no
aerobicyes86.931no
halophileno92.24no
spore-formingno85.801no
thermophileno92.236no
glucose-utilyes69.025no
flagellatedno99.039no
glucose-fermentno93.121no

External links

@ref: 11444

culture collection no.: DSM 43995, ATCC 19250, NCTC 10042, TMC 1482, JCM 15661, CCUG 28011, CCUG 31306, CIP 104035, CNCTC 7303

straininfo link

  • @ref: 77769
  • straininfo: 44545

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics8513789Structure of a novel glycopeptidolipid antigen containing a O-methylated serine isolated from Mycobacterium xenopi. Complete 1H-NMR and 13C-NMR assignment.Riviere M, Auge S, Vercauteren J, Wisingerova E, Puzo GEur J Biochem10.1111/j.1432-1033.1993.tb17935.x1993Amino Acid Sequence, Antigens, Bacterial/*chemistry, Carbohydrate Conformation, Carbohydrate Sequence, Chromatography, Thin Layer, Glycoconjugates/*chemistry/isolation & purification, *Magnetic Resonance Spectroscopy, Methylation, Molecular Sequence Data, Mycobacterium/*chemistry, Serine/*analysisEnzymology
Genetics14715774Novel mass spectrometry-based tool for genotypic identification of mycobacteria.Lefmann M, Honisch C, Bocker S, Storm N, von Wintzingerode F, Schlotelburg C, Moter A, van den Boom D, Gobel UBJ Clin Microbiol10.1128/JCM.42.1.339-346.20042004Genotype, Mycobacterium/classification/*genetics, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methodsPhylogeny
Pathogenicity26142475Time-kill kinetics of slowly growing mycobacteria common in pulmonary disease.Ferro BE, van Ingen J, Wattenberg M, van Soolingen D, Mouton JWJ Antimicrob Chemother10.1093/jac/dkv1802015Amikacin/pharmacology, Anti-Bacterial Agents/*pharmacology, Clarithromycin/pharmacology, Dose-Response Relationship, Drug, Drug Resistance, Bacterial, Microbial Sensitivity Tests, Mutation, Mutation Rate, Mycobacterium avium/*drug effects/genetics, Mycobacterium xenopi/*drug effects, Time FactorsEnzymology
Genetics32139563Complete Genome Sequence of Mycobacterium xenopi JCM15661(T), Obtained Using Nanopore and Illumina Sequencing Technologies.Yoshida M, Fukano H, Asakura T, Hisatsune J, Hoshino YMicrobiol Resour Announc10.1128/MRA.01583-192020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11444Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43995)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43995
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
34458Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15898
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
77769Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44545.1StrainInfo: A central database for resolving microbial strain identifiers
123974Curators of the CIPCollection of Institut Pasteur (CIP 104035)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104035