Strain identifier

BacDive ID: 8465

Type strain: Yes

Species: Mycobacterium chubuense

Strain Designation: 48013

Strain history: CIP <- 2000, JCM <- M. Tsukamura: strain 48013

NCBI tax ID(s): 1800 (species)

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General

@ref: 11603

BacDive-ID: 8465

DSM-Number: 44219

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

description: Mycobacterium chubuense 48013 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from garden soil.

NCBI tax id

  • NCBI tax id: 1800
  • Matching level: species

strain history

@refhistory
11603<- M. Goodfellow, OI-CHU <- NCTC <- M. Tsukamura, 5517
67770NCTC 10819 <-- M. Tsukamura 5517.
118262CIP <- 2000, JCM <- M. Tsukamura: strain 48013

doi: 10.13145/bacdive8465.20230509.8.1

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 chubuense
  • full scientific name: Mycobacterium chubuense (ex Tsukamura 1973) Tsukamura 1981

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium chubuense

@ref: 11603

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium chubuense

full scientific name: Mycobacterium chubuense (ex Tsukamura 1973) Tsukamura 1981 emend. Nouioui et al. 2018

strain designation: 48013

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
118262rod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19850Pale orange10-14 days5006
19850Pale orange10-14 daysBHI
19850Pale orange10-14 daysBUG
19850Pale orange10-14 daysMB7H9
537972 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11603LÖWENSTEIN-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
11603MIDDLEBROOK 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
19850BUGyes
19850BHIyes
198505006yesMedium: 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
19850MB7H9yesName: Middlebrook 7H9 (MB7H9) Broth Base Composition: Middelbrook 7H9 Broth Base 4.7 g/l Glycerol 2.0 g/l Casaminoacids 11.0 g/l Yeast extract 5.5 g/l Tween80 (20%) 2.5 g/l OADC-Enrichment 100 ml Agar 15.0 g/l Preparation: Dissolve in Milli-Q-H2O. Before Use add 10% OADC stock solution Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Maintenance and revitalization Organisms: 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
36351MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118262CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
19850positiveoptimum37mesophilic
11603positivegrowth37mesophilic
36351positivegrowth37mesophilic
53797positivegrowth30-37mesophilic
67770positivegrowth37mesophilic
118262positivegrowth22-30
118262nogrowth10psychrophilic
118262nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
53797aerobe
118262obligate aerobe

spore formation

@refspore formationconfidence
69481no94
69480no99.917

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
118262606565hippurate+hydrolysis
11826217632nitrate+reduction
11826216301nitrite-reduction
11826217632nitrate-respiration
683794853esculin-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 118262
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 118262
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68379gelatinase-
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
118262oxidase-
118262beta-galactosidase-3.2.1.23
118262gelatinase-
118262amylase-
118262DNase-
118262caseinase-3.4.21.50
118262tween esterase+
118262gamma-glutamyltransferase-2.3.2.2
118262lecithinase-
118262lipase-
118262protease-
118262urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
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 NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControl
19850-+-----------------
11603+-----+--+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19850-++----------------
11603-+/-+-++/-+/---+/-----+-----
118262-++-++---++---+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118262------------+------+-+-+---++------+-+--------+-------------+---+----------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11603garden soilChubu hospitalJapanJPNAsia
53797Garden soil
67770Garden soil in the National Chubu HospitalObu, Aichi Pref.JapanJPNAsia
118262Environment, Soil

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

taxonmaps

  • @ref: 69479
  • File name: preview.99_6383.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_115;97_219;98_419;99_6383&stattab=map
  • Last taxonomy: Mycolicibacterium
  • 16S sequence: X55596
  • Sequence Identity:
  • Total samples: 4905
  • soil counts: 1619
  • aquatic counts: 1667
  • animal counts: 1470
  • plant counts: 149

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116031Risk group (German classification)
198501Risk group (German classification)
1182621Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium chubuense 16S ribosomal RNA gene, partial sequenceAF4805971472ena1800
20218M.chubuense 16S ribosomal RNA, partX555961458ena1800
20218Mycobacterium chubuense strain CIP 106810 16S ribosomal RNA gene, partial sequenceAF547912540ena1800

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium chubuense NCTC10819GCA_900453455contigncbi1800
66792Mycobacterium chubuense strain DSM 442191800.3wgspatric1800
66792Mycobacterium chubuense strain DSM 442191800.5wgspatric1800
66792Mycolicibacterium chubuense strain NCTC108191800.9wgspatric1800
66792Mycobacterium chubuense NCTC 108192808606776draftimg1800
66792Mycolicibacterium chubuense DSM 442192630968491draftimg1800
67770Mycolicibacterium chubuense DSM 44219GCA_001044255scaffoldncbi1800
67770Mycolicibacterium chubuense DSM 44219GCA_002086595contigncbi1800

GC content

  • @ref: 67770
  • GC-content: 69.2
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
motileno93.083no
gram-positiveyes90.472no
anaerobicno99.353no
aerobicyes91.919yes
halophileno93.171no
spore-formingno85.81no
glucose-utilyes89.178no
flagellatedno98.546no
thermophileno99.308yes
glucose-fermentno90.979no

External links

@ref: 11603

culture collection no.: DSM 44219, ATCC 27278, JCM 6374, NCTC 10819, CCUG 37670, CIP 106810, JCM 16420, KCTC 19712

straininfo link

  • @ref: 77860
  • straininfo: 38908

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics26079817Characterization 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, DNAPhylogeny
34591668Whole-Genome Sequencing of Alcaligenes faecalis HZ01, with Potential to Inhibit Nontuberculous Mycobacterial Growth.Fernandes HMZ, Conceicao EC, da Silva SP, Machado E, Sisco MC, Sharma A, Lima KVB, da Conceicao ML, da Silva Carvalho AC, Miranda KR, Silva Duarte R, Alviano DS, da Silva Dias RCMicrobiol Resour Announc10.1128/MRA.00521-212021
Phylogeny36282561Mycolicibacterium aurantiacum sp. nov. and Mycolicibacterium xanthum sp. nov., two novel actinobacteria isolated from mangrove sediments.Pan X, Li Z, Huang S, Huang Y, Wang Q, Tao Z, Hu WInt J Syst Evol Microbiol10.1099/ijsem.0.0055952022*Actinobacteria, Bacterial Typing Techniques, Base Composition, Copper, DNA, Bacterial/genetics, Fatty Acids/chemistry, Kerosene, Nucleic Acid Hybridization, Nucleotides, Oxidoreductases/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Geologic SedimentsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11603Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44219)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44219
19850Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44219.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
36351Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18982
53797Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37670)https://www.ccug.se/strain?id=37670
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
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)
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
77860Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38908.1StrainInfo: A central database for resolving microbial strain identifiers
118262Curators of the CIPCollection of Institut Pasteur (CIP 106810)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106810