Strain identifier

BacDive ID: 8559

Type strain: Yes

Species: Mycobacterium insubricum

Strain Designation: FI-06250

Strain history: CIP <- 2007, E. Tortoli, Careggi Hosp., Firenze, Italy: strain FI-06250

NCBI tax ID(s): 444597 (species)

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General

@ref: 12379

BacDive-ID: 8559

DSM-Number: 45132

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, human pathogen

description: Mycobacterium insubricum FI-06250 is a microaerophile, mesophilic, Gram-positive human pathogen that builds an aerial mycelium and was isolated from human sputum.

NCBI tax id

  • NCBI tax id: 444597
  • Matching level: species

strain history

@refhistory
12379<- E. Tortoli; FI-06250 <- C. Sturla
67770CIP 109609 <-- E. Tortoli Fl-06250.
120138CIP <- 2007, E. Tortoli, Careggi Hosp., Firenze, Italy: strain FI-06250

doi: 10.13145/bacdive8559.20230509.8.1

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 insubricum
  • full scientific name: Mycobacterium insubricum Tortoli et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium insubricum

@ref: 12379

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium insubricum

full scientific name: Mycobacterium insubricum Tortoli et al. 2009

strain designation: FI-06250

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
29000positiveno
69480no94.69
69480positive100
120138no

colony morphology

@refcolony colorincubation periodmedium used
20168Light ivory (1014)10-14 daysISP 2
20168Light ivory (1014)10-14 daysISP 3
20168Light ivory (1014)10-14 daysISP 4
20168Light ivory (1014)10-14 daysISP 5
20168Light ivory (1014)10-14 daysISP 6
20168Ivory (1014)10-14 daysISP 7
606812 days

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20168yesAerial MyceliumLight ivoryISP 2
20168noISP 3
20168noISP 4
20168noISP 5
20168noISP 6
20168noISP 7

pigmentation

  • @ref: 29000
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12379MIDDLEBROOK 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
20168ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20168ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20168ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20168ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20168ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20168ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
120138CIP Medium 267yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=267

culture temp

@refgrowthtypetemperaturerange
12379positivegrowth37mesophilic
20168positiveoptimum37
29000positivegrowth25-37
29000positiveoptimum31
60681positivegrowth37
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60681microaerophile
120138obligate aerobe

spore formation

@refspore formationconfidence
29000no
69481no90
69480no99.983

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2016817234glucose+
2016822599arabinose+/-
2016817992sucrose+/-
2016818222xylose+/-
2016817268myo-inositol+/-
2016829864mannitol+/-
2016828757fructose+/-
2016826546rhamnose+/-
2016816634raffinose+/-
2016862968cellulose-
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12013817632nitrate-reduction
12013816301nitrite-reduction
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: 120138
  • 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
120138oxidase-
120138catalase+1.11.1.6
120138urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382naphthol-AS-BI-phosphohydrolase+
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-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20168-------------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20168-+++++---++---+--+-
120138-++-+-----+---------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120138----------+++------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12379human sputumNorthernItalyITAEurope
60681Human sputumGallarateItalyITAEurope
67770Sputum of a patient with pleural effusionVareseItalyITAEurope
120138Human, SputumNorthernItalyITAEurope

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Sputum

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12379yes, in single cases1Risk group (German classification)
1201381Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12379
  • description: Mycobacterium insubricum strain FI-06250 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence
  • accession: EU605695
  • length: 1995
  • database: ena
  • NCBI tax ID: 444597

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium insubricum JCM 16366GCA_010731615completencbi444597
66792Mycolicibacterium insubricum strain JCM 16366444597.11completepatric444597
66792Mycolicibacterium insubricum DSM 45132GCA_025821225contigncbi444597

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno90no
motileno95.562no
flagellatedno98.542no
gram-positiveyes90.614yes
anaerobicno98.001yes
aerobicyes77.309yes
halophileno93.344no
spore-formingno90.873yes
glucose-utilyes78.117no
thermophileno97.966no
glucose-fermentno92.08yes

External links

@ref: 12379

culture collection no.: DSM 45132, CIP 109609, CCUG 55636, JCM 16366

straininfo link

@refstraininfo
77942362818
77943409545

literature

  • topic: Phylogeny
  • Pubmed-ID: 19502346
  • title: Mycobacterium insubricum sp. nov.
  • authors: Tortoli E, Baruzzo S, Heijdra Y, Klenk HP, Lauria S, Mariottini A, van Ingen J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.003459-0
  • year: 2009
  • mesh: Adult, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Base Sequence, DNA, Bacterial/analysis, DNA, Ribosomal Spacer/analysis/chemistry/genetics, Humans, Middle Aged, Molecular Sequence Data, Mycobacterium/*classification/genetics/isolation & purification/physiology, Mycobacterium Infections/microbiology, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Restriction Mapping, Sequence Analysis, DNA, Species Specificity, Sputum/*microbiology, Young Adult
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
12379Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45132)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45132
20168Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45132.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
29000Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2543328776041
60681Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55636)https://www.ccug.se/strain?id=55636
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
77942Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362818.1StrainInfo: A central database for resolving microbial strain identifiers
77943Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID409545.1StrainInfo: A central database for resolving microbial strain identifiers
120138Curators of the CIPCollection of Institut Pasteur (CIP 109609)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109609