Strain identifier
BacDive ID: 23165
Type strain: 
Species: Nocardioides albertanoniae
Strain Designation: CD40127
Strain history: <- V. Jurado, Inst. de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain; CD40127 <- L. Trobajo
NCBI tax ID(s): 1175486 (species)
version 8.1 (current version)
General
@ref: 19302
BacDive-ID: 23165
DSM-Number: 25218
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped
description: Nocardioides albertanoniae CD40127 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from green biofilm from the wall of a catacombe.
NCBI tax id
- NCBI tax id: 1175486
- Matching level: species
strain history
- @ref: 19302
- history: <- V. Jurado, Inst. de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain; CD40127 <- L. Trobajo
doi: 10.13145/bacdive23165.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Propionibacteriales
- family: Nocardioidaceae
- genus: Nocardioides
- species: Nocardioides albertanoniae
- full scientific name: Nocardioides albertanoniae Alias-Villegas et al. 2013
@ref: 19302
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Nocardioides
species: Nocardioides albertanoniae
full scientific name: Nocardioides albertanoniae Alias-Villegas et al. 2013
strain designation: CD40127
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30766 | positive | 1.3 µm | 0.7 µm | rod-shaped | no | |
| 69480 | no | 93.367 | ||||
| 69480 | positive | 100 |
pigmentation
- @ref: 30766
- production: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 19302 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf | |
| 19302 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 19302 | positive | growth | 28 | mesophilic |
| 30766 | positive | growth | 10-30 | |
| 30766 | positive | optimum | 25 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 30766
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30766 | no | |
| 69480 | no | 98.176 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30766 | NaCl | positive | growth | 0-10 % |
| 30766 | NaCl | positive | optimum | 2 % |
observation
- @ref: 30766
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30766 | 22599 | arabinose | + | carbon source |
| 30766 | 24265 | gluconate | + | carbon source |
| 30766 | 17234 | glucose | + | carbon source |
| 30766 | 25115 | malate | + | carbon source |
| 30766 | 17306 | maltose | + | carbon source |
| 30766 | 29864 | mannitol | + | carbon source |
| 30766 | 37684 | mannose | + | carbon source |
| 30766 | 506227 | N-acetylglucosamine | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30766 | acid phosphatase | + | 3.1.3.2 |
| 30766 | alkaline phosphatase | + | 3.1.3.1 |
| 30766 | catalase | + | 1.11.1.6 |
| 30766 | gelatinase | + |
Isolation, sampling and environmental information
isolation
- @ref: 19302
- sample type: green biofilm from the wall of a catacombe
- geographic location: Rome, Domitilla Catacombs
- country: Italy
- origin.country: ITA
- continent: Europe
isolation source categories
| Cat1 | Cat2 |
|---|---|
| #Engineered | #Built environment |
| #Environmental | #Biofilm |
Safety information
risk assessment
- @ref: 19302
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19302
- description: Nocardioides albertanoniae partial 16S rRNA gene, type strain CD40127T
- accession: HE801966
- length: 1407
- database: ena
- NCBI tax ID: 1175486
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Nocardioides albertanoniae DSM 25218 | GCA_006716315 | contig | ncbi | 1175486 |
| 66792 | Nocardioides albertanoniae strain DSM 25218 | 1175486.3 | wgs | patric | 1175486 |
| 66792 | Nocardioides albertanoniae DSM 25218 | 2816332112 | draft | img | 1175486 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 19302 | 69.7 | high performance liquid chromatography (HPLC) |
| 30766 | 69.7 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 81 | no |
| motile | no | 96.427 | yes |
| gram-positive | yes | 92.663 | yes |
| anaerobic | no | 99.349 | yes |
| halophile | no | 81.88 | no |
| spore-forming | no | 68.383 | yes |
| flagellated | no | 97.44 | no |
| glucose-util | yes | 89.603 | yes |
| aerobic | yes | 92.623 | no |
| thermophile | no | 98.495 | no |
| glucose-ferment | no | 93.177 | no |
External links
@ref: 19302
culture collection no.: DSM 25218, CECT 8014
straininfo link
- @ref: 87399
- straininfo: 387810
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22798645 | Nocardioides albertanoniae sp. nov., isolated from Roman catacombs. | Alias-Villegas C, Jurado V, Laiz L, Miller AZ, Saiz-Jimenez C | Int J Syst Evol Microbiol | 10.1099/ijs.0.043885-0 | 2012 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rome, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis | Genetics |
| 35855324 | Psi-Footprinting approach for the identification of protein synthesis inhibitor producers. | Handel F, Kulik A, Wex KW, Berscheid A, Saur JS, Winkler A, Wibberg D, Kalinowski J, Brotz-Oesterhelt H, Mast Y | NAR Genom Bioinform | 10.1093/nargab/lqac055 | 2022 |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 19302 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25218) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25218 | |||
| 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 | |||
| 30766 | 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 | 27097 | 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) | |||
| 87399 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID387810.1 | StrainInfo: A central database for resolving microbial strain identifiers |