Strain identifier

BacDive ID: 8454

Type strain: Yes

Species: Mycobacterium hodleri

Strain Designation: EMI 2

Strain history: CIP <- 1996, DSMZ <- M. Kleespies: strain EMI 2

NCBI tax ID(s): 1305625 (strain), 49897 (species)

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General

@ref: 11581

BacDive-ID: 8454

DSM-Number: 44183

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, rod-shaped

description: Mycobacterium hodleri EMI 2 is an aerobe, mesophilic, rod-shaped bacterium that was isolated from fluoranthene and benzapyren contaminated soil.

NCBI tax id

NCBI tax idMatching level
49897species
1305625strain

strain history

@refhistory
11581<- M. Kleespies, EMI 2
67770LMG 19253 <-- D. Springael <-- DSM 44183 <-- M. Kleespies EMI 2.
119927CIP <- 1996, DSMZ <- M. Kleespies: strain EMI 2

doi: 10.13145/bacdive8454.20241212.9.2

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 hodleri
  • full scientific name: Mycobacterium hodleri Kleespies et al. 1996

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium hodleri

@ref: 11581

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium hodleri

full scientific name: Mycobacterium hodleri Kleespies et al. 1996

strain designation: EMI 2

type strain: yes

Morphology

cell morphology

@refcell shapemotilityconfidence
119927rod-shapedno
69480no95.75

colony morphology

  • @ref: 54103
  • incubation period: 4 days

multimedia

  • @ref: 11581
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44183.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11581PEPTONE MEAT EXTRACT GLYCEROL AGAR (DSMZ Medium 250)yeshttps://mediadive.dsmz.de/medium/250Name: PEPTONE MEAT EXTRACT GLYCEROL AGAR (DSMZ Medium 250) Composition: Agar 20.0 g/l Proteose peptone no. 3 5.0 g/l Meat extract 3.0 g/l Glycerol Distilled water
11581MIDDLEBROOK 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
36386MEDIUM 55 - for Mycobacteriumyes
119927CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperature
11581positivegrowth37
36386positivegrowth25
54103positivegrowth30
67770positivegrowth28
119927positivegrowth10-30
119927nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
54103aerobe
119927obligate aerobe

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2), MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
119927606565hippurate+hydrolysis
11992717632nitrate-reduction
11992716301nitrite-reduction
11992717632nitrate-respiration

metabolite production

  • @ref: 119927
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
119927oxidase-
119927beta-galactosidase+3.2.1.23
119927gelatinase-
119927amylase-
119927DNase-
119927caseinase-3.4.21.50
119927catalase+1.11.1.6
119927tween esterase+
119927gamma-glutamyltransferase-2.3.2.2
119927lecithinase-
119927lipase-
119927protease-
119927urease+3.5.1.5
68382cystine arylamidase+3.4.11.3

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119927-+++++++--++---++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
11581fluoranthene and benzapyren contaminated soil
54103Contaminant of fluoranthrene and benzapyrinGermanyDEUEurope
67770Soil contaminated with fluoranthene and benzopyreneGermanyDEUEuropenear Jülich
119927Fluoranthene and benzapyrin contaminatedGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5434.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_115;97_3229;98_4057;99_5434&stattab=map
  • Last taxonomy: Mycolicibacterium
  • 16S sequence: X93184
  • Sequence Identity:
  • Total samples: 2769
  • soil counts: 1352
  • aquatic counts: 579
  • animal counts: 443
  • plant counts: 395

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115811Risk group (German classification)
1199271Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium hodleri strain CIP 104909 16S ribosomal RNA gene, partial sequenceAF547936540nuccore49897
20218Mycolicibacterium hodleri strain DSM 44183 16S-23S ribosomal RNA intergenic spacer, complete sequenceKC010494456nuccore49897
20218M.hodleri 16S rRNA geneX931841459nuccore49897

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium hodleri JCM 12141GCA_001313805contigncbi1305625
66792Mycolicibacterium hodleri JCM 121411305625.4wgspatric1305625
66792Mycolicibacterium hodleri JCM 121412681813036draftimg1305625
66792Mycolicibacterium hodleri DSM 44183GCA_025822245scaffoldncbi49897

GC content

  • @ref: 11581
  • GC-content: 73
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes78.616no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no86.622yes
69480spore-formingspore-formingAbility to form endo- or exosporesno78.565no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.699yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.565yes
69480flagellatedmotile2+Ability to perform flagellated movementno95.75no

External links

@ref: 11581

culture collection no.: DSM 44183, CIP 104909T, CCUG 38151, CIP 104909, JCM 12141, LMG 19253

straininfo link

  • @ref: 77850
  • straininfo: 13219

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8782676Mycobacterium hodleri sp. nov., a new member of the fast-growing mycobacteria capable of degrading polycyclic aromatic hydrocarbons.Kleespies M, Kroppenstedt RM, Rainey FA, Webb LE, Stackebrandt EInt J Syst Bacteriol10.1099/00207713-46-3-6831996Base Sequence, DNA, Bacterial, Fluorenes/metabolism, Molecular Sequence Data, Mycobacterium/*classification/genetics/isolation & purification/metabolism, Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolism, Soil MicrobiologyMetabolism
Phylogeny23728378Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., two rapidly growing members of the genus Mycobacterium.Zhang DF, Chen X, Zhang XM, Zhi XY, Yao JC, Jiang Y, Xiong Z, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.050567-02013Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/chemistry, Genes, Bacterial, Geologic Sediments/*microbiology, Molecular Sequence Data, Multilocus Sequence Typing, Mycobacterium/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Oceans and Seas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, United Arab EmiratesGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11581Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44183)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44183
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
36386Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16870
54103Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38151)https://www.ccug.se/strain?id=38151
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)
77850Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13219.1StrainInfo: A central database for resolving microbial strain identifiers
119927Curators of the CIPCollection of Institut Pasteur (CIP 104909)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104909