Strain identifier

BacDive ID: 8444

Type strain: Yes

Species: Mycobacterium nonchromogenicum

Strain history: CIP <- 2000, JCM <- M.Tsukamura: strain 09003, Mycobacterium terrae

NCBI tax ID(s): 1782 (species)

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General

@ref: 11562

BacDive-ID: 8444

DSM-Number: 44164

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

description: Mycobacterium nonchromogenicum DSM 44164 is an obligate aerobe, mesophilic, rod-shaped human pathogen that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1782
  • Matching level: species

strain history

@refhistory
11562<- ATCC <- M. Tsukamura, 317 (Mycobacterium terrae)
67770M. Tsukamura 09003 (=317).
121346CIP <- 2000, JCM <- M.Tsukamura: strain 09003, Mycobacterium terrae

doi: 10.13145/bacdive8444.20230509.8.1

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 nonchromogenicum
  • full scientific name: Mycobacterium nonchromogenicum Tsukamura 1965 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacter nonchromogenicus

@ref: 11562

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium nonchromogenicum

full scientific name: Mycobacterium nonchromogenicum Tsukamura 1965

type strain: yes

Morphology

cell morphology

  • @ref: 121346
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
20009Light ivory (1015)10-14 days5006
20009Light ivory (1015)10-14 daysMB7H10
20009Light ivory (1015)10-14 daysMB7H11

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11562PEPTONE 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
11562MIDDLEBROOK 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
20009MB7H10yesName: 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
20009MB7H11yesName: 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
200095006yesMedium: 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
36353MEDIUM 112 - for JanibacteryesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);Casamino acids (5.000 g);Ca
121346CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
20009positiveoptimum37mesophilic
11562positivegrowth37mesophilic
36353positivegrowth37mesophilic
67770positivegrowth37mesophilic
121346positivegrowth22-37
121346nogrowth10psychrophilic
121346nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121346
  • oxygen tolerance: obligate aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
121346606565hippurate-hydrolysis
12134617632nitrate+reduction
12134616301nitrite-reduction
12134617632nitrate-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: 121346
  • 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
121346oxidase-
121346beta-galactosidase+3.2.1.23
121346gelatinase-
121346catalase+1.11.1.6
121346gamma-glutamyltransferase-2.3.2.2
121346urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20009-+-+-++----------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20009+++-+++--++-+-++--+
121346++++++---++-+-++----

Isolation, sampling and environmental information

isolation

@refsample type
11562soil
49063Soil
67770Soil
121346Environment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_473.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_312;97_346;98_391;99_473&stattab=map
  • Last taxonomy: Mycolicibacter
  • 16S sequence: X52928
  • Sequence Identity:
  • Total samples: 3339
  • soil counts: 1370
  • aquatic counts: 1264
  • animal counts: 528
  • plant counts: 177

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
11562yesyes2Risk group (German classification)
200091German classification
1213461Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium nonchromogenicum strain ATCC 19530 16S ribosomal RNA gene, partial sequenceDQ0584061374ena1782
20218Mycobacterium nonchromogenicum strain ATCC 19530 16S ribosomal RNA gene, partial sequenceJN571171479ena1782
20218M.nonchromogenicum 16S ribosomal RNAM295651376ena1782
20218M.nonchromogenicum 16S ribosomal RNA geneM59270146ena1782
20218Mycobacterium nonchromogenicum 16S rRNA geneX529281466ena1782
20218Mycobacterium nonchromogenicum CCUG:28009 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceHM584724278ena1782
20218Mycobacterium nonchromogenicum strain DSM 44164 16S ribosomal RNA gene, partial sequenceAF547952556ena1782

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium nonchromogenicum strain DSM 441641782.7wgspatric1782
67770Mycolicibacter nonchromogenicus DSM 44164GCA_002101775contigncbi1782
66792Mycolicibacter nonchromogenicus DSM 44164GCA_025821265scaffoldncbi1782

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.367no
gram-positiveyes92.414no
anaerobicno99.386no
aerobicyes93.636no
halophileno91.207no
spore-formingno90.32no
thermophileno97.777yes
glucose-utilyes60.862no
flagellatedno98.828no
glucose-fermentno91.352yes

External links

@ref: 11562

culture collection no.: DSM 44164, ATCC 19530, ATCC 23067, JCM 6364, NCTC 10424, TMC 1481, CCUG 28009, CIP 106811

straininfo link

  • @ref: 77842
  • straininfo: 44548

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology15722145Multicenter evaluation of mycobacteria identification by PCR restriction enzyme analysis in laboratories from Latin America and the Caribbean.Leao SC, Bernardelli A, Cataldi A, Zumarraga M, Robledo J, Realpe T, Mejia GI, da Silva Telles MA, Chimara E, Velazco M, Fernandez J, Rodrigues PA, Guerrero MI, Leon CI, Porras TB, Rastogi N, Goh KS, Suffys P, da Silva Rocha A, dos Santos Netto D, Ritacco V, Lopez B, Barrera L, Palomino JC, Martin A, Portaels FJ Microbiol Methods10.1016/j.mimet.2004.11.0152004Bacterial Proteins/chemistry/genetics, Chaperonin 60, Chaperonins/chemistry/genetics, DNA, Bacterial/chemistry/genetics, Guadeloupe, Humans, Mycobacterium/genetics/*isolation & purification, Mycobacterium Infections/*diagnosis, Polymerase Chain Reaction/*methods/standards, Restriction Mapping, South AmericaPathogenicity
Phylogeny16738122Mycobacterium arupense sp. nov., a non-chromogenic bacterium isolated from clinical specimens.Cloud JL, Meyer JJ, Pounder JI, Jost KC, Sweeney A, Carroll KC, Woods GLInt J Syst Evol Microbiol10.1099/ijs.0.64194-02006Base Sequence, Humans, Molecular Sequence Data, Mycobacterium/*classification/*genetics/isolation & purification, Mycobacterium Infections, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Tendons/*microbiologyPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11562Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44164)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44164
20009Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44164.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
36353Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18983
49063Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28009)https://www.ccug.se/strain?id=28009
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
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
77842Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44548.1StrainInfo: A central database for resolving microbial strain identifiers
121346Curators of the CIPCollection of Institut Pasteur (CIP 106811)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106811