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BacDive ID 8433
Type strain
Strain Designation 4388, 47001
Culture col. no. CCUG 37669 CIP 106803 KCTC 19097 DSM 44075 ATCC 27023 JCM 6372 NCTC 10778 4388 47001 HAMBI 2272 5 more
NCBI tax ID(s) 1807
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 10 (current version):
version 10 (current version)

General

@ref: 11474

BacDive-ID: 8433

DSM-Number: 44075

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

description: Mycobacterium obuense 4388 is an aerobe, mesophilic, Gram-positive prokaryote 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/bacdive8433.20251217.10

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: kingdom/bacillati
  • keyword: phylum/actinomycetota
  • 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
121377negativegrowth10
121377negativegrowth45

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

metabolite production

  • @ref: 121377
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-glucosidase+3.2.1.20
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51
68382alpha-galactosidase-3.2.1.22
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
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-
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68382beta-glucuronidase-3.2.1.31
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68379catalase+1.11.1.6
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
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

Interaction and safety

risk assessment

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

Sequence information

Genome sequences

  • @ref: 67770
  • description: ASM104424v1 assembly for Mycolicibacterium obuense DSM 44075
  • assembly level: contig
  • INSDC accession: GCA_001044245
  • BV-BRC accession: 1807.14
  • IMG accession: 2636415843
  • NCBI tax ID: 1807
  • score: 66.81

16S sequences

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

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

Literature

@ref: 11474

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

straininfo link

  • @ref: 126262
  • straininfo: 45780

literature

Pubmed-IDtitleauthorsjournalDOIyearmeshtopictopic2
8332525Compilation of small ribosomal subunit RNA structures.Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R.Nucleic Acids Res10.1093/nar/21.13.30251993genetics, Databases, Factual
26067960Draft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient Sputum.Greninger AL, Cunningham G, Hsu ED, Yu JM, Chiu CY, Miller S.Genome Announc10.1128/genomea.00612-152015
26079817Characterization of Three Mycobacterium spp. with Potential Use in Bioremediation by Genome Sequencing and Comparative Genomics.Das S, Pettersson BM, Behra PR, Ramesh M, Dasgupta S, Bhattacharya A, Kirsebom LAGenome Biol Evol10.1093/gbe/evv1112015Biodegradation, 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, DNAGeneticsPhylogeny
29497402Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera.Gupta RS, Lo B, Son J.Front Microbiol10.3389/fmicb.2018.000672018Phylogenomic Analysis, Mycobacterium Classification, Abscessus-chelonae Clade, Conserved Signature Indels And Signature Proteins, Fortuitum-vaccae Clade, Slow-growing And Fast-growing Mycobacteria, Terrae Clade, Triviale CladePhylogeny
31002048Mycobacterium obuense Bacteremia in a Patient with Pneumonia.Luis BAL, Diaz-Lomeli P, Gomez-Albarran LP, Martinez-Gamboa A, Ponce-de-Leon A.Emerg Infect Dis10.3201/eid2505.1802082019Bacteria, Lung, Immunotherapy, Pathogenicity, Pneumonia, bacteremia, Mexico, Respiratory Infections, Blood Cultures, Tuberculosis And Other Mycobacteria, Mycobacteria Obuense, microbiology, diagnosis, microbiology, diagnosis, microbiology, Nontuberculous Mycobacteria
31138571In Vitro Activities of Bedaquiline and Delamanid against Nontuberculous Mycobacteria Isolated in Beijing, China.Yu X, Gao X, Li C, Luo J, Wen S, Zhang T, Ma Y, Dong L, Wang F, Huang H.Antimicrob Agents Chemother10.1128/aac.00031-192019Susceptibility, Nontuberculous Mycobacteria, Bedaquiline, Delamanid, pharmacology, pharmacology, pharmacology, drug effects, pharmacologyPathogenicity
35958142In vitro and intracellular inhibitory activities of nosiheptide against Mycobacterium abscessus.Zhu R, Yu X, Zhang T, Kong Y, Wang F, Jia J, Xue Y, Huang H.Front Microbiol10.3389/fmicb.2022.9263612022Cytotoxicity, Susceptibility, Nosiheptide, Mycobacterium Abscessus, Intracellular Bactericidal Activity
36250885In Vitro Activity of the Sudapyridine (WX-081) against Non-Tuberculous Mycobacteria Isolated in Beijing, China.Zhu R, Shang Y, Chen S, Xiao H, Ren R, Wang F, Xue Y, Li L, Li Y, Chu N, Huang H.Microbiol Spectr10.1128/spectrum.01372-222022Antimicrobial activity, Non-tuberculous Mycobacteria, Sudapyridine, Mycobacterium Infections, Nontuberculous, Nontuberculous Mycobacteria

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
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
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
126262A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer10.1093/database/baaf059StrainInfo—the central database for linked microbial strain identifiers

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