Strain identifier

BacDive ID: 8534

Type strain: Yes

Species: Mycobacterium florentinum

Strain Designation: FI-93171

Strain history: CIP <- 2004, E. Tortoli, San Raffaele Scientific Inst., Florence, Italy: strain FI-93171

NCBI tax ID(s): 292462 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 12121

BacDive-ID: 8534

DSM-Number: 44852

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, ovoid-shaped

description: Mycobacterium florentinum FI-93171 is a microaerophile, mesophilic, ovoid-shaped bacterium that was isolated from cervical lymph node of a girl.

NCBI tax id

  • NCBI tax id: 292462
  • Matching level: species

strain history

@refhistory
12121<- E. Tortoli; FI-93171
67770CIP 108409 <-- E. Tortoli FI-93171.
119401CIP <- 2004, E. Tortoli, San Raffaele Scientific Inst., Florence, Italy: strain FI-93171

doi: 10.13145/bacdive8534.20230509.8.1

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 florentinum
  • full scientific name: Mycobacterium florentinum Tortoli et al. 2005

@ref: 12121

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium florentinum

full scientific name: Mycobacterium florentinum Tortoli et al. 2005 emend. Nouioui et al. 2018

strain designation: FI-93171

type strain: yes

Morphology

cell morphology

@refcell shapemotilityconfidencegram stain
31408ovoid-shapedno
69480no95.988
69480100positive
119401rod-shapedno

pigmentation

  • @ref: 31408
  • production: no

multimedia

  • @ref: 12121
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44852.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12121MIDDLEBROOK 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
12121LÖWENSTEIN-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
36340MEDIUM 93 - for Mycobacterium avium subsp. sylvaticumyesDistilled water make up to (900.000 ml);Glycerol (4.500 ml);Middlebrook7H10 agar (17.000 g);Middelbrook OADC enrichment (100.000 ml)
119401CIP Medium 93yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=93

culture temp

@refgrowthtypetemperaturerange
12121positivegrowth37mesophilic
31408positivegrowth25-37
31408positiveoptimum31
36340positivegrowth30
59080positivegrowth37
67770positivegrowth30mesophilic
119401positivegrowth22-30
119401nogrowth10psychrophilic
119401nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59080microaerophile
119401obligate aerobe

spore formation

@refspore formationconfidence
31408no
69481no98
69480no99.919

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3140817632nitrate+reduction
119401606565hippurate-hydrolysis
11940117632nitrate+reduction
11940116301nitrite-reduction
11940117632nitrate-respiration

antibiotic resistance

  • @ref: 119401
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119401
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31408catalase+1.11.1.6
31408urease+3.5.1.5
119401oxidase-
119401beta-galactosidase-3.2.1.23
119401gelatinase-
119401amylase-
119401DNase+
119401caseinase-3.4.21.50
119401catalase+1.11.1.6
119401tween esterase+
119401gamma-glutamyltransferase-2.3.2.2
119401lecithinase-
119401lipase-
119401protease-
119401urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
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
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119401--++-+--------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationisolation date
12121cervical lymph node of a girlItalyITAEurope
59080Human lymph nodeItalyITAEurope1993Florence
67770Excised lymph node of a 6-year-old girl with lymphadenopathyItalyITAEurope
119401Human, Cervical lymphnodeItalyITAEurope1993

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
121212Risk group (German classification)
1194011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium florentinum strain DSM 44852 16S ribosomal RNA gene, partial sequenceDQ350154475ena292462
12121Mycobacterium florentinum 16S rRNA gene and ITS1, type strain FI-93171TAJ6162301788ena292462

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium florentinum JCM 14740GCA_010730355completencbi292462
66792Mycobacterium florentinum strain DSM 44852292462.3wgspatric292462
66792Mycobacterium florentinum strain JCM 14740292462.10completepatric292462
66792Mycobacterium florentinum DSM 448522865192396draftimg292462
67770Mycobacterium florentinum DSM 44852GCA_002101635contigncbi292462
66792Mycobacterium florentinum DSM 44852GCA_025823305scaffoldncbi292462

GC content

  • @ref: 67770
  • GC-content: 66.4
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileno94.056yes
flagellatedno98.565no
gram-positiveyes89.459no
anaerobicno99.05yes
aerobicyes90.518yes
halophileno94.845no
spore-formingno86.496yes
glucose-utilyes70.185no
thermophileno97.472yes
glucose-fermentno92.46no

External links

@ref: 12121

culture collection no.: DSM 44852, CIP 108409, CCUG 50992, JCM 14740

straininfo link

  • @ref: 77920
  • straininfo: 139000

literature

  • topic: Phylogeny
  • Pubmed-ID: 15879240
  • title: Mycobacterium florentinum sp. nov., isolated from humans.
  • authors: Tortoli E, Rindi L, Goh KS, Katila ML, Mariottini A, Mattei R, Mazzarelli G, Suomalainen S, Torkko P, Rastogi N
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63485-0
  • year: 2005
  • mesh: Adult, Aged, Anti-Bacterial Agents/pharmacology, Bacterial Proteins/genetics, Cell Wall/chemistry, Chaperonin 60, Chaperonins/genetics, Child, Chromatography, Gas, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA, Ribosomal Spacer, Drug Resistance, Bacterial, Feces/microbiology, Female, Genes, rRNA, Humans, Lipids/analysis/isolation & purification, Lymph Nodes/*microbiology, Male, Molecular Sequence Data, Mycobacterium/*classification/cytology/*isolation & purification/physiology, Phylogeny, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sputum/*microbiology
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12121Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44852)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44852
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
31408Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127717
36340Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6028
59080Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50992)https://www.ccug.se/strain?id=50992
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/
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
77920Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID139000.1StrainInfo: A central database for resolving microbial strain identifiers
119401Curators of the CIPCollection of Institut Pasteur (CIP 108409)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108409