Strain identifier
BacDive ID: 8534
Type strain:
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)
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
@ref | history |
---|---|
12121 | <- E. Tortoli; FI-93171 |
67770 | CIP 108409 <-- E. Tortoli FI-93171. |
119401 | CIP <- 2004, E. Tortoli, San Raffaele Scientific Inst., Florence, Italy: strain FI-93171 |
doi: 10.13145/bacdive8534.20241212.9.2
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
@ref | cell shape | motility |
---|---|---|
31408 | ovoid-shaped | no |
119401 | rod-shaped | no |
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
@ref | name | growth | link | composition |
---|---|---|---|---|
12121 | MIDDLEBROOK MEDIUM (DSMZ Medium 645) | yes | https://mediadive.dsmz.de/medium/645 | Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water |
12121 | LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354) | yes | https://mediadive.dsmz.de/medium/354 | Name: 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 |
36340 | MEDIUM 93 - for Mycobacterium avium subsp. sylvaticum | yes | Distilled water make up to (900.000 ml);Glycerol (4.500 ml);Middlebrook7H10 agar (17.000 g);Middelbrook OADC enrichment (100.000 ml) | |
119401 | CIP Medium 93 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=93 |
culture temp
@ref | growth | type | temperature |
---|---|---|---|
12121 | positive | growth | 37 |
31408 | positive | growth | 25-37 |
31408 | positive | optimum | 31 |
36340 | positive | growth | 30 |
59080 | positive | growth | 37 |
67770 | positive | growth | 30 |
119401 | positive | growth | 22-30 |
119401 | no | growth | 10 |
119401 | no | growth | 45 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
59080 | microaerophile |
119401 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31408 | no | |
69481 | no | 98 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31408 | 17632 | nitrate | + | reduction |
119401 | 606565 | hippurate | - | hydrolysis |
119401 | 17632 | nitrate | + | reduction |
119401 | 16301 | nitrite | - | reduction |
119401 | 17632 | nitrate | - | 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
@ref | value | activity | ec |
---|---|---|---|
31408 | catalase | + | 1.11.1.6 |
31408 | urease | + | 3.5.1.5 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
119401 | oxidase | - | |
119401 | beta-galactosidase | - | 3.2.1.23 |
119401 | gelatinase | - | |
119401 | amylase | - | |
119401 | DNase | + | |
119401 | caseinase | - | 3.4.21.50 |
119401 | catalase | + | 1.11.1.6 |
119401 | tween esterase | + | |
119401 | gamma-glutamyltransferase | - | 2.3.2.2 |
119401 | lecithinase | - | |
119401 | lipase | - | |
119401 | protease | - | |
119401 | urease | + | 3.5.1.5 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119401 | - | - | + | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | sampling date | geographic location | isolation date |
---|---|---|---|---|---|---|---|
12121 | cervical lymph node of a girl | Italy | ITA | Europe | |||
59080 | Human lymph node | Italy | ITA | Europe | 1993 | Florence | |
67770 | Excised lymph node of a 6-year-old girl with lymphadenopathy | Italy | ITA | Europe | |||
119401 | Human, Cervical lymphnode | Italy | ITA | Europe | 1993 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Infection | #Patient | |
#Host Body-Site | #Organ | #Lymph node |
#Host | #Human | #Female |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
12121 | 2 | Risk group (German classification) |
119401 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Mycobacterium florentinum strain DSM 44852 16S ribosomal RNA gene, partial sequence | DQ350154 | 475 | nuccore | 292462 |
12121 | Mycobacterium florentinum 16S rRNA gene and ITS1, type strain FI-93171T | AJ616230 | 1788 | nuccore | 292462 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycobacterium florentinum JCM 14740 | GCA_010730355 | complete | ncbi | 292462 |
66792 | Mycobacterium florentinum strain DSM 44852 | 292462.3 | wgs | patric | 292462 |
66792 | Mycobacterium florentinum strain JCM 14740 | 292462.10 | complete | patric | 292462 |
66792 | Mycobacterium florentinum DSM 44852 | 2865192396 | draft | img | 292462 |
67770 | Mycobacterium florentinum DSM 44852 | GCA_002101635 | contig | ncbi | 292462 |
66792 | Mycobacterium florentinum DSM 44852 | GCA_025823305 | scaffold | ncbi | 292462 |
GC content
- @ref: 67770
- GC-content: 66.4
- method: genome sequence analysis
Genome-based predictions
predictions
@ref | trait | model | description | prediction | confidence | training_data |
---|---|---|---|---|---|---|
69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 98 | no |
69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 89.761 | no |
69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.751 | yes |
69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 78.784 | no |
69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 58.282 | yes |
69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.385 | no |
69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 87 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
12121 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44852) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44852 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
31408 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 27717 | ||
36340 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6028 | |||||
59080 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 50992) | https://www.ccug.se/strain?id=50992 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68382 | Automatically annotated from API zym | ||||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
77920 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID139000.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
119401 | Curators of the CIP | Collection of Institut Pasteur (CIP 108409) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108409 |