Strain identifier

BacDive ID: 8493

Type strain: Yes

Species: Mycobacterium parmense

Strain Designation: Fi-14400, MUP-1182, F1-3198

Strain history: CIP <- 2002, E. Tortoli, Azienda Hosp., Firenze, Italy: strain F1-3198 <- F. Fanti

NCBI tax ID(s): 185642 (species)

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General

@ref: 11750

BacDive-ID: 8493

DSM-Number: 44553

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

description: Mycobacterium parmense Fi-14400 is a microaerophile, mesophilic, rod-shaped human pathogen that was isolated from cervical lymphnode of a child.

NCBI tax id

  • NCBI tax id: 185642
  • Matching level: species

strain history

@refhistory
11750<- E. Tortoli; Fi-14400 <- F. Fanti
67770CIP 107385 <-- E. Tortoli <-- F. Fanti MUP 1182.
121600CIP <- 2002, E. Tortoli, Azienda Hosp., Firenze, Italy: strain F1-3198 <- F. Fanti

doi: 10.13145/bacdive8493.20230509.8.1

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 parmense
  • full scientific name: Mycobacterium parmense Fanti et al. 2004

@ref: 11750

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium parmense

full scientific name: Mycobacterium parmense Fanti et al. 2004 emend. Nouioui et al. 2018

strain designation: Fi-14400, MUP-1182, F1-3198

type strain: yes

Morphology

cell morphology

@refcell shapemotilityconfidencegram stain
29969rod-shapedno
69480no93.664
69480100positive
121600rod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19868Zinc yellow10-14 days5006
19868Zinc yellow10-14 daysMB7H10
19868Zinc yellow10-14 daysMB7H11

multimedia

  • @ref: 11750
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44553.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11750MIDDLEBROOK 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
19868MB7H10yesName: 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
19868MB7H11yesName: 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
198685006yesMedium: 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
121600CIP Medium 267yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=267

culture temp

@refgrowthtypetemperaturerange
19868positiveoptimum37mesophilic
11750positivegrowth37mesophilic
29969positivegrowth25-37mesophilic
29969positiveoptimum31mesophilic
67770positivegrowth37mesophilic
121600positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121600
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
29969no
69480no98.805

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2996953426tween 80+carbon source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
121600606565hippurate+hydrolysis
12160017632nitrate-reduction
12160016301nitrite-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

@refChebi-IDmetaboliteproduction
6836935581indoleno
12160035581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
29969catalase+1.11.1.6
29969urease+3.5.1.5
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
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
121600oxidase-
121600beta-galactosidase-3.2.1.23
121600alcohol dehydrogenase-1.1.1.1
121600catalase+1.11.1.6
121600gamma-glutamyltransferase-2.3.2.2
121600lysine decarboxylase-4.1.1.18
121600ornithine decarboxylase-4.1.1.17
121600urease+3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382valine arylamidase-
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
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    59085C14:03.214
    59085C16:024.816
    59085C18:03.218
    59085C10:0 2 methyl2.110.321
    59085C16:1 ω7c/C15:0 ISO 2OH2.815.85
    59085C16:1 ω9c9.215.774
    59085C17:1 ω7c6.416.818
    59085C18:1 ω9c30.317.769
    59085C20:0 alcohol (C20:0 2OH alc)8.818.835
    59085TBSA 10Me18:09.218.392
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19868---+---------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19868++++-----++----+---
11750+/-++-+-+/---++---+-----
121600-++-+-----+---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
11750----++--------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
11750cervical lymphnode of a childParmaItalyITAEurope
59085Human lymph nodeParmaItalyITAEurope2001
67770Cervical lymph node from a 3-year-old girl with a local swelling of the left submandibular regionParmaItalyITAEurope
121600Human, Cervical lymph node (child)ParmaItalyITAEurope1999

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body-Site#Organ#Lymph node
#Host#Human#Child

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
11750yes, in single cases1Risk group (German classification)
198681Risk group (German classification)
1216001Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium parmense strain CIP 107385 16S ribosomal RNA gene, partial sequenceAY943212495ena185642
20218Mycobacterium parmense strain CIP 107385 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequenceHM0222011795ena185642
11750Mycobacterium parmense 16S ribosomal RNA gene, complete sequenceAF4668211533ena185642

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium parmense JCM 14742GCA_010730575completencbi185642
66792Mycobacterium parmense strain DSM 44553185642.3wgspatric185642
66792Mycobacterium parmense strain JCM 14742185642.10completepatric185642
66792Mycobacterium parmense DSM 445532865418304draftimg185642
67770Mycobacterium parmense DSM 44553GCA_002102335contigncbi185642
66792Mycobacterium parmense DSM 44553GCA_025822965scaffoldncbi185642

GC content

  • @ref: 67770
  • GC-content: 68.4
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno86no
motileno95.308no
flagellatedno98.807yes
gram-positiveyes90.332no
anaerobicno99.315no
aerobicyes90.397no
halophileno92.26no
spore-formingno84.03yes
glucose-utilyes57.183yes
thermophileno97.911yes
glucose-fermentno91.601yes

External links

@ref: 11750

culture collection no.: DSM 44553, CIP 107385, MUP 1182, CCUG 50998, JCM 14742

straininfo link

  • @ref: 77887
  • straininfo: 132790

literature

  • topic: Phylogeny
  • Pubmed-ID: 15280280
  • title: Mycobacterium parmense sp. nov.
  • authors: Fanti F, Tortoli E, Hall L, Roberts GD, Kroppenstedt RM, Dodi I, Conti S, Polonelli L, Chezzi C
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02760-0
  • year: 2004
  • mesh: Arylsulfatases/metabolism, Bacterial Typing Techniques, Child, Preschool, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry, Genes, rRNA, Humans, Lipids/analysis, Lymph Nodes/*microbiology, Molecular Sequence Data, Mycobacterium/*classification/cytology/isolation & purification/physiology, Nitrate Reductase, Nitrate Reductases/metabolism, Phylogeny, Polysorbates/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Staining and Labeling, Temperature, Urease/metabolism, beta-Glucosidase/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
11750Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44553)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44553
19868Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44553.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
29969Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126338
59085Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50998)https://www.ccug.se/strain?id=50998
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/
68369Automatically annotated from API 20NE
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)
77887Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132790.1StrainInfo: A central database for resolving microbial strain identifiers
121600Curators of the CIPCollection of Institut Pasteur (CIP 107385)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107385