Strain identifier
BacDive ID: 3232
Type strain: 
Species: Corynebacterium massiliense
Strain Designation: 5402485
Strain history: CCUG 53857 <-- V. Roux; Timone Hosp., France; 5402485.
NCBI tax ID(s): 1121364 (strain), 441501 (species)
version 9.1 (current version)
General
@ref: 16813
BacDive-ID: 3232
DSM-Number: 45435
keywords: genome sequence, 16S sequence, Bacteria, aerobe
description: Corynebacterium massiliense 5402485 is an aerobe bacterium that was isolated from human infection, osteoarticular.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 441501 | species |
| 1121364 | strain |
strain history
| @ref | history |
|---|---|
| 16813 | <- CCUG; CCUG 53857 <- V. Roux, Timone Hospital, Marseille |
| 67770 | CCUG 53857 <-- V. Roux; Timone Hosp., France; 5402485. |
doi: 10.13145/bacdive3232.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Mycobacteriales
- family: Corynebacteriaceae
- genus: Corynebacterium
- species: Corynebacterium massiliense
- full scientific name: Corynebacterium massiliense Merhej et al. 2009
@ref: 16813
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Corynebacteriaceae
genus: Corynebacterium
species: Corynebacterium massiliense
full scientific name: Corynebacterium massiliense Merhej et al. 2009 emend. Nouioui et al. 2018
strain designation: 5402485
type strain: yes
Morphology
cell morphology
- @ref: 69480
- motility: no
- confidence: 95.5
colony morphology
- @ref: 60038
- incubation period: 2 days
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 16813 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
| 16813 | TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a) | yes | https://mediadive.dsmz.de/medium/535a | Name: TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a) Composition: None 50.0 g/l Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 16813 | positive | growth | 37 |
| 60038 | positive | growth | 37 |
| 67770 | positive | growth | 37 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 60038 | aerobe |
| 60038 | microaerophile |
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 16813 | human infection, osteoarticular | Marseille, Timone Hospital | France | FRA | Europe | |
| 60038 | Human infection,osteoarticular | Marseille,Timone hospital | France | FRA | Europe | 2005-11-01 |
| 67770 | Human hip joint fluid of a 84-year-old patient | Marseilles | France | FRA | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Disease | |
| #Host | #Human | |
| #Host Body-Site | #Other | #Bone |
taxonmaps
- @ref: 69479
- File name: preview.99_2389.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1287;97_1528;98_1861;99_2389&stattab=map
- Last taxonomy: Corynebacterium massiliense subclade
- 16S sequence: EF217056
- Sequence Identity:
- Total samples: 4341
- soil counts: 33
- aquatic counts: 109
- animal counts: 4177
- plant counts: 22
Safety information
risk assessment
- @ref: 16813
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16813
- description: Corynebacterium massiliensis strain 5402485 16S ribosomal RNA gene, partial sequence
- accession: EF217056
- length: 1443
- database: nuccore
- NCBI tax ID: 1121364
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Corynebacterium massiliense DSM 45435 | 1121364.3 | wgs | patric | 1121364 |
| 66792 | Corynebacterium massiliense DSM 45435 | 2524023165 | draft | img | 1121364 |
| 67770 | Corynebacterium massiliense DSM 45435 | GCA_000420605 | scaffold | ncbi | 1121364 |
| 66792 | Corynebacterium massiliense DSM 45435 | GCA_028609805 | complete | ncbi | 1121364 |
GC content
- @ref: 67770
- GC-content: 65
- 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 | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 89.516 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 93.785 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 54.403 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 83.031 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 96.5 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 95.5 | no |
External links
@ref: 16813
culture collection no.: DSM 45435, CCUG 53857, CIP 109423, CSUR P19, JCM 32212
straininfo link
- @ref: 72746
- straininfo: 398501
literature
- topic: Phylogeny
- Pubmed-ID: 19567562
- title: Corynebacterium timonense sp. nov. and Corynebacterium massiliense sp. nov., isolated from human blood and human articular hip fluid.
- authors: Merhej V, Falsen E, Raoult D, Roux V
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.005827-0
- year: 2009
- mesh: Anaerobiosis, Bacterial Typing Techniques, Blood/*microbiology, Cluster Analysis, Corynebacterium/*classification/genetics/*isolation & purification/physiology, Corynebacterium Infections/*microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hip Joint/*microbiology, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Pathogenicity
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 16813 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45435) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45435 | |
| 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 | |
| 60038 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 53857) | https://www.ccug.se/strain?id=53857 | |
| 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/ | ||
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |
| 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 | |
| 72746 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398501.1 | StrainInfo: A central database for resolving microbial strain identifiers |