Strain identifier

BacDive ID: 8481

Type strain: Yes

Species: Mycobacterium elephantis

Strain Designation: 484, 484T

Strain history: CIP <- 2000, J. G. Magee, PHLS North, Newcastle, UK: strain 484T <- M. Yates, Public Health La., Dulwich Hosp., London, UK <- N.U. Horadagoda, Univ. Perodeniya, Sri Lanka

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

@ref: 11709

BacDive-ID: 8481

DSM-Number: 44368

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

description: Mycobacterium elephantis 484 is an obligate aerobe, mesophilic human pathogen that was isolated from lung abscess, elephant.

NCBI tax id

NCBI tax idMatching level
81858species
1335622strain

strain history

@refhistory
11709<- J.G. Magee, Public Health Lab., Newcastle upon Tyne, UK, 484 <- M. Yates, Public Health Laboratory, Dulwich Hospital, London UK <- N.U. Horadagoda, Univ. of Perodeniya, Sri Lanka
67770CIP 106831 <-- J. G. Magee 484 <-- M. Yates <-- N. U. Horadagoda.
119006CIP <- 2000, J. G. Magee, PHLS North, Newcastle, UK: strain 484T <- M. Yates, Public Health La., Dulwich Hosp., London, UK <- N.U. Horadagoda, Univ. Perodeniya, Sri Lanka

doi: 10.13145/bacdive8481.20230509.8.1

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 elephantis
  • full scientific name: Mycobacterium elephantis Shojaei et al. 2000
  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium elephantis

@ref: 11709

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium elephantis

full scientific name: Mycobacterium elephantis Shojaei et al. 2000

strain designation: 484, 484T

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.662
69480100positive
119006norod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19858Saffron yellow10-14 days5006
19858Saffron yellow10-14 daysMB7H10
19858Saffron yellow10-14 daysMB7H11

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11709MIDDLEBROOK 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
19858MB7H10yesName: 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
19858MB7H11yesName: 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
198585006yesMedium: 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
36352MEDIUM 55 - for Mycobacteriumyes
119006CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
19858positiveoptimum37mesophilic
11709positivegrowth37mesophilic
36352positivegrowth37mesophilic
67770positivegrowth37mesophilic
119006positivegrowth30-45
119006nogrowth10psychrophilic
119006nogrowth22psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119006
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no90
69480no99.994

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
119006606565hippurate-hydrolysis
11900617632nitrate+reduction
11900616301nitrite-reduction
11900617632nitrate-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: 119006
  • 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
119006oxidase-
119006beta-galactosidase+3.2.1.23
119006gelatinase-
119006amylase+
119006DNase-
119006caseinase-3.4.21.50
119006catalase+1.11.1.6
119006tween esterase+
119006gamma-glutamyltransferase+2.3.2.2
119006lecithinase-
119006lipase+
119006protease-
119006urease+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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19858-+++-----+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19858+++-++++-++---++---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119006------------+----------------------------------------------------+----------------------+-------+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11709lung abscess, elephantSri LankaLKAAsia
67770Lung abscess of an elephant
119006Elephant, lung abscessSri LankaLKAAsia

isolation source categories

Cat1Cat2Cat3
#Host#Mammals
#Host Body-Site#Oral cavity and airways#Lung
#Host Body-Site#Other#Abscess

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
11709yesyes2Risk group (German classification)
198582Risk group (German classification)
1190061Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium elephantis 16S rRNA gene, partialAJ0107471517ena81858
20218Mycobacterium elephantis strain CIP 106831 16S ribosomal RNA gene, partial sequenceAF547919544ena81858

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium elephantis DSM 443681335622.5wgspatric1335622
67770Mycolicibacterium elephantis DSM 44368GCA_004014805contigncbi1335622
66792Mycolicibacterium elephantis DSM 44368GCA_025822495scaffoldncbi81858

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno90no
motileno95.443no
gram-positiveyes91.698no
anaerobicno99.339no
halophileno83.668no
spore-formingno80.416no
thermophileno98.606yes
glucose-utilyes79.784no
aerobicyes87.922no
flagellatedno99.043no
glucose-fermentno89.72no

External links

@ref: 11709

culture collection no.: DSM 44368, JCM 12406, CIP 106831

straininfo link

  • @ref: 77875
  • straininfo: 50594

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11034492Mycobacterium elephantis sp. nov., a rapidly growing non-chromogenic Mycobacterium isolated from an elephant.Shojaei H, Magee JG, Freeman R, Yates M, Horadagoda NU, Goodfellow MInt J Syst Evol Microbiol10.1099/00207713-50-5-18172000Animals, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Elephants/*microbiology, Lung Abscess/microbiology/*veterinary, Molecular Sequence Data, Mycobacterium/*classification/growth & development/*isolation & purification/physiology, Mycobacterium Infections/microbiology/*veterinary, Phenotype, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny11923337Phenotypic and molecular characterization of clinical isolates of Mycobacterium elephantis from human specimens.Turenne C, Chedore P, Wolfe J, Jamieson F, May K, Kabani AJ Clin Microbiol10.1128/JCM.40.4.1230-1236.20022002Adult, Aged, Aged, 80 and over, *Bacterial Typing Techniques, Base Sequence, Female, Humans, Male, Middle Aged, Molecular Sequence Data, Mycobacterium/*classification/*genetics/isolation & purification, Mycobacterium Infections/*microbiology, Mycolic Acids/analysis, Phenotype, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Restriction Mapping/methods, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11709Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44368)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44368
19858Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44368.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
36352Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19005
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
77875Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50594.1StrainInfo: A central database for resolving microbial strain identifiers
119006Curators of the CIPCollection of Institut Pasteur (CIP 106831)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106831