Strain identifier
BacDive ID: 23139
Type strain: 
Species: Mycobacterium fragae
Strain Designation: Fiocruz-INCQS/CMRVS P4051, HF 8705
Strain history: <- E. Tortoli, Milano, Italy; HF 8705 <- J. P. Ramos <- C. L. Campelo, Mycobacteria Sector, Central Laboratory of Ceará State, Brazil
NCBI tax ID(s): 1260918 (species)
version 8.1 (current version)
General
@ref: 19373
BacDive-ID: 23139
DSM-Number: 45731
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, rod-shaped, human pathogen
description: Mycobacterium fragae Fiocruz-INCQS/CMRVS P4051 is a mesophilic, rod-shaped human pathogen that was isolated from sputum of a Brazilian patient with a lung infection.
NCBI tax id
- NCBI tax id: 1260918
- Matching level: species
strain history
- @ref: 19373
- history: <- E. Tortoli, Milano, Italy; HF 8705 <- J. P. Ramos <- C. L. Campelo, Mycobacteria Sector, Central Laboratory of Ceará State, Brazil
doi: 10.13145/bacdive23139.20230509.8.1
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 fragae
- full scientific name: Mycobacterium fragae Ramos et al. 2013
@ref: 19373
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium fragae
full scientific name: Mycobacterium fragae Ramos et al. 2013 emend. Nouioui et al. 2018
strain designation: Fiocruz-INCQS/CMRVS P4051, HF 8705
type strain: yes
Morphology
cell morphology
| @ref | cell shape | motility | confidence | gram stain |
|---|---|---|---|---|
| 30887 | rod-shaped | no | ||
| 69480 | no | 95.968 | ||
| 69480 | 100 | positive |
pigmentation
- @ref: 30887
- production: no
Culture and growth conditions
culture medium
- @ref: 19373
- name: MIDDLEBROOK MEDIUM (DSMZ Medium 645)
- growth: yes
- link: https://mediadive.dsmz.de/medium/645
- composition: Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 19373 | positive | growth | 37 | mesophilic |
| 30887 | positive | growth | 30-37 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 94 |
| 69480 | no | 99.916 |
enzymes
- @ref: 30887
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 19373
- sample type: sputum of a Brazilian patient with a lung infection
- geographic location: northeastern Brazil, Ceará State
- country: Brazil
- origin.country: BRA
- continent: Middle and South America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Disease | |
| #Infection | #Patient | |
| #Host Body-Site | #Oral cavity and airways | #Lung |
| #Host Body Product | #Fluids | #Sputum |
Safety information
risk assessment
- @ref: 19373
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19373
- description: Mycobacterium fragae strain HF8705 16S ribosomal RNA gene, partial sequence
- accession: JQ898451
- length: 1452
- database: ena
- NCBI tax ID: 1260918
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Mycobacterium fragae DSM 45731 | GCA_002102185 | contig | ncbi | 1260918 |
| 66792 | Mycobacterium fragae strain DSM 45731 | 1260918.5 | wgs | patric | 1260918 |
| 66792 | Mycobacterium fragae DSM 45731 | 2865371644 | draft | img | 1260918 |
| 66792 | Mycobacterium fragae DSM 45731 | GCA_025823245 | scaffold | ncbi | 1260918 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 94 | no |
| motile | no | 94.712 | no |
| gram-positive | yes | 91.095 | no |
| anaerobic | no | 98.943 | no |
| aerobic | yes | 87.696 | no |
| halophile | no | 93.566 | no |
| spore-forming | no | 86.721 | no |
| thermophile | no | 97.996 | yes |
| glucose-util | yes | 64.826 | no |
| flagellated | no | 98.586 | no |
| glucose-ferment | no | 91.35 | no |
External links
@ref: 19373
culture collection no.: DSM 45731
straininfo link
- @ref: 87373
- straininfo: 405646
literature
- topic: Phylogeny
- Pubmed-ID: 23264503
- title: Mycobacterium fragae sp. nov., a non-chromogenic species isolated from human respiratory specimens.
- authors: Ramos JP, Campos CED, Caldas PCS, Ferreira NV, Boas da Silva MV, Redner P, Campelo CL, Vale SF, Barroso EC, Medeiros RFM, Montes FCOF, Galvao TC, Tortoli E
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.046862-0
- year: 2012
- mesh: Bacterial Proteins/genetics, Brazil, Chaperonin 60/genetics, DNA, Bacterial/genetics, Genes, Bacterial, Humans, Lung Diseases/microbiology, Molecular Sequence Data, Mycobacterium/*classification/genetics/isolation & purification, Mycobacterium Infections/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sputum/*microbiology
- topic2: Pathogenicity
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 19373 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45731) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45731 | |||
| 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 | |||
| 30887 | 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 | 27217 | 28776041 | |
| 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) | |||
| 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 | |||
| 87373 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405646.1 | StrainInfo: A central database for resolving microbial strain identifiers |