Strain identifier
BacDive ID: 8346
Type strain: 
Species: Mycobacterium longobardum
Strain Designation: FI-07034
Strain history: CCUG 58460 <-- E. Tortoli; Careggi Hosp., Italy; FI-07034 <-- V. Penati <-- S. Pierdomenico.
NCBI tax ID(s): 1108812 (species)
version 8.1 (current version)
General
@ref: 16583
BacDive-ID: 8346
DSM-Number: 45394
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, coccus-shaped, human pathogen
description: Mycobacterium longobardum FI-07034 is a microaerophile, mesophilic, coccus-shaped human pathogen that was isolated from sputum from an Italian patient suffering from broncho-pneumonitis.
NCBI tax id
- NCBI tax id: 1108812
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16583 | <- E. Tortoli, Firenze, Italy; FI-07034 <- V. Penati <- S. Pierdomenico |
| 67770 | CCUG 58460 <-- E. Tortoli; Careggi Hosp., Italy; FI-07034 <-- V. Penati <-- S. Pierdomenico. |
doi: 10.13145/bacdive8346.20230509.8.1
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 longobardum
- full scientific name: Mycobacterium longobardum Tortoli et al. 2013
synonyms
- @ref: 20215
- synonym: Mycolicibacter longobardus
@ref: 16583
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium longobardum
full scientific name: Mycobacterium longobardum Tortoli et al. 2013 emend. Nouioui et al. 2018
strain designation: FI-07034
type strain: yes
Morphology
cell morphology
| @ref | cell shape | motility | confidence | gram stain |
|---|---|---|---|---|
| 30561 | coccus-shaped | |||
| 69480 | no | 95.083 | ||
| 69480 | 100 | positive |
colony morphology
- @ref: 61692
- incubation period: 3-5 days
pigmentation
- @ref: 30561
- production: no
Culture and growth conditions
culture medium
- @ref: 16583
- 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 |
|---|---|---|---|---|
| 16583 | positive | growth | 37 | mesophilic |
| 30561 | positive | growth | 25-37 | mesophilic |
| 30561 | positive | optimum | 31 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 61692
- oxygen tolerance: microaerophile
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30561 | no | |
| 69481 | no | 99 |
| 69480 | no | 99.932 |
metabolite utilization
- @ref: 30561
- Chebi-ID: 17632
- metabolite: nitrate
- utilization activity: +
- kind of utilization tested: reduction
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30561 | arylsulfatase | + | 3.1.6.1 |
| 30561 | catalase | + | 1.11.1.6 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 16583 | sputum from an Italian patient suffering from broncho-pneumonitis | Lombardy | Italy | ITA | Europe |
| 61692 | Human clinical sample | Italy | ITA | Europe | |
| 67770 | Sputum from an Italian patient suffering from broncho-pneumonitis | Lombardy | Italy | ITA | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Inflammation | |
| #Infection | #Patient | |
| #Host Body Product | #Fluids | #Sputum |
Safety information
risk assessment
- @ref: 16583
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16583
- description: Mycobacterium longobardum strain DSM 45394 16S ribosomal RNA gene, partial sequence
- accession: JN571166
- length: 1500
- database: ena
- NCBI tax ID: 1108812
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Mycobacterium longobardum strain DSM 45394 | 1108812.3 | wgs | patric | 1108812 |
| 66792 | Mycolicibacter longobardus DSM 45394 | 2865385185 | draft | img | 1108812 |
| 67770 | Mycolicibacter longobardus DSM 45394 | GCA_002102265 | contig | ncbi | 1108812 |
| 66792 | Mycolicibacter longobardus DSM 45394 | GCA_025823135 | scaffold | ncbi | 1108812 |
GC content
- @ref: 67770
- GC-content: 67.9
- method: genome sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| motile | no | 94.203 | no |
| flagellated | no | 98.809 | no |
| gram-positive | yes | 92.019 | no |
| anaerobic | no | 99.377 | yes |
| aerobic | yes | 86.535 | yes |
| halophile | no | 90.337 | no |
| spore-forming | no | 85.178 | yes |
| thermophile | no | 98.679 | yes |
| glucose-util | yes | 61.4 | no |
| glucose-ferment | no | 92.638 | no |
External links
@ref: 16583
culture collection no.: DSM 45394, CCUG 58460, JCM 32217
straininfo link
- @ref: 77748
- straininfo: 407449
literature
- topic: Phylogeny
- Pubmed-ID: 22447702
- title: Survey of 150 strains belonging to the Mycobacterium terrae complex and description of Mycobacterium engbaekii sp. nov., Mycobacterium heraklionense sp. nov. and Mycobacterium longobardum sp. nov.
- authors: Tortoli E, Gitti Z, Klenk HP, Lauria S, Mannino R, Mantegani P, Mariottini A, Neonakis I
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.038737-0
- year: 2012
- mesh: Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Molecular Sequence Data, Mycolic Acids/analysis, Nontuberculous Mycobacteria/*classification/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16583 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45394) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45394 | |||
| 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 | |||
| 30561 | 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 | 26892 | 28776041 | |
| 61692 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 58460) | https://www.ccug.se/strain?id=58460 | |||
| 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/ | ||||
| 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 | |||
| 77748 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407449.1 | StrainInfo: A central database for resolving microbial strain identifiers |