Strain identifier

BacDive ID: 8433

Type strain: Yes

Species: Mycobacterium obuense

Strain Designation: 4388, 47001

Strain history: CIP <- 2000, JCM <- M. Tsukamura: strain 47001

NCBI tax ID(s): 1807 (species)

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General

@ref: 11474

BacDive-ID: 8433

DSM-Number: 44075

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

description: Mycobacterium obuense 4388 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sputum in a case of pulmonary disease.

NCBI tax id

  • NCBI tax id: 1807
  • Matching level: species

strain history

@refhistory
11474<- S. Rüsch-Gerdes <- ATCC <- M. Tsukamura, 4388 <- N. Kita
67771<- CCUG <- JCM, RIKEN, Saitama, Japan 02 Apr 1997 <- 1987, M Tsukamura 47001
67770M. Tsukamura 47001.
121377CIP <- 2000, JCM <- M. Tsukamura: strain 47001

doi: 10.13145/bacdive8433.20250331.9.3

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 obuense
  • full scientific name: Mycobacterium obuense (ex Tsukamura and Mizuno 1971) Tsukamura and Mizuno 1981

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium obuense

@ref: 11474

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium obuense

full scientific name: Mycobacterium obuense (ex Tsukamura and Mizuno 1971) Tsukamura and Mizuno 1981 emend. Nouioui et al. 2018

strain designation: 4388, 47001

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
67771positive
121377rod-shapedno
125438positive91.135
125439positive99.4

colony morphology

@refcolony colorincubation periodmedium used
19842Pure orange10-14 days5006
19842Pure orange10-14 daysMB7H10
19842Pure orange10-14 daysMB7H11
537963 days

multimedia

  • @ref: 11474
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44075.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11474LÖWENSTEIN-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
11474MIDDLEBROOK 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
19842MB7H10yesName: 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
19842MB7H11yesName: 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
198425006yesMedium: 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
36381MEDIUM 55 - for Mycobacteriumyes
121377CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperature
19842positiveoptimum37
11474positivegrowth37
36381positivegrowth30
53796positivegrowth30
67770positivegrowth37
67771positivegrowth37
121377positivegrowth22-37
121377nogrowth10
121377nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
53796aerobe
67771aerobe
121377obligate aerobe
125439obligate aerobe98.9

observation

@refobservation
67770quinones: MK-9(H2)
67771quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837928087glycogen-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837917634D-glucose-fermentation
683795291gelatin-hydrolysis
6837917632nitrate-reduction
121377606565hippurate-hydrolysis
12137717632nitrate-reduction
12137716301nitrite-reduction
12137717632nitrate-respiration

metabolite production

  • @ref: 121377
  • 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
68382alpha-glucosidase+3.2.1.20
68382alpha-galactosidase-3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
121377oxidase-
121377beta-galactosidase-3.2.1.23
121377gelatinase-
121377amylase-
121377DNase-
121377caseinase-3.4.21.50
121377catalase+1.11.1.6
121377tween esterase-
121377gamma-glutamyltransferase+2.3.2.2
121377lecithinase-
121377lipase-
121377protease-
121377urease+3.5.1.5
68379gelatinase-
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379catalase+1.11.1.6
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379pyrrolidonyl arylamidase-3.4.19.3

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
19842-+----+--+---------
53796---+--+-+-----------+
11474---+--+-------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19842-++++++--++-+-++---
53796+-+-+++--++---+-----
11474--+-++/-+/---+----+-----
121377-++-+++--++---+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121377-+-----+----+--------------------+---+--------------+-------------------------------+-------+------

Isolation, sampling and environmental information

isolation

@refsample type
11474sputum in a case of pulmonary disease
53796Soil
67770Soil
67771From sputum in a case of pulmonary disease
121377Environment, Soil

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Host Body Product#Fluids#Sputum

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
11474yes, in single cases1Risk group (German classification)
198421Risk group (German classification)
1213771Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium obuense strain CIP 106803 16S ribosomal RNA gene, partial sequenceAF547954540nuccore1807
11474M.obuense 16S ribosomal RNA, partX555971458nuccore1807

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium obuense strain DSM 440751807.14wgspatric1807
66792Mycolicibacterium obuense DSM 440752636415843draftimg1807
67770Mycolicibacterium obuense DSM 44075GCA_001044245contigncbi1807

GC content

  • @ref: 67770
  • GC-content: 68
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.135yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.374no
125438spore-formingspore-formingAbility to form endo- or exosporesno65.306no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.5yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.212yes
125438motile2+flagellatedAbility to perform flagellated movementno85.871no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes66
125439BacteriaNetmotilityAbility to perform movementno89.7
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.9

External links

@ref: 11474

culture collection no.: CCUG 37669, CIP 106803, KCTC 19097, DSM 44075, ATCC 27023, JCM 6372, NCTC 10778, HAMBI 2272

straininfo link

  • @ref: 77832
  • straininfo: 45780

literature

  • topic: Genetics
  • Pubmed-ID: 26079817
  • title: Characterization of Three Mycobacterium spp. with Potential Use in Bioremediation by Genome Sequencing and Comparative Genomics.
  • authors: Das S, Pettersson BM, Behra PR, Ramesh M, Dasgupta S, Bhattacharya A, Kirsebom LA
  • journal: Genome Biol Evol
  • DOI: 10.1093/gbe/evv111
  • year: 2015
  • mesh: Biodegradation, Environmental, Copper/metabolism, Gene Transfer, Horizontal, Genes, Bacterial, *Genome, Bacterial, Genomics, Molecular Sequence Data, Mycobacterium/classification/*genetics/metabolism, Oxygenases/genetics, Phylogeny, RNA, Untranslated/genetics, Sequence Alignment, Sequence Analysis, DNA
  • topic2: Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11474Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44075)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44075
19842Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44075.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
36381Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18973
53796Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37669)https://www.ccug.se/strain?id=37669
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
77832Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45780.1StrainInfo: A central database for resolving microbial strain identifiers
121377Curators of the CIPCollection of Institut Pasteur (CIP 106803)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106803
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1