Strain identifier
BacDive ID: 11235
Type strain:
Species: Nocardiopsis valliformis
Strain history: CGMCC 4.2135 <-- R. Yang et al. HBUM 20028.
NCBI tax ID(s): 1246448 (strain), 239974 (species)
General
@ref: 12253
BacDive-ID: 11235
DSM-Number: 45023
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Nocardiopsis valliformis DSM 45023 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil of saline.
NCBI tax id
NCBI tax id | Matching level |
---|---|
239974 | species |
1246448 | strain |
strain history
@ref | history |
---|---|
12253 | <- Z. Liping; HBUM 20028 <- C.-L. Jiang |
67770 | CGMCC 4.2135 <-- R. Yang et al. HBUM 20028. |
doi: 10.13145/bacdive11235.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Nocardiopsidaceae
- genus: Nocardiopsis
- species: Nocardiopsis valliformis
- full scientific name: Nocardiopsis valliformis Yang et al. 2008
@ref: 12253
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardiopsaceae
genus: Nocardiopsis
species: Nocardiopsis valliformis
full scientific name: Nocardiopsis valliformis Yang et al. 2008
type strain: yes
Morphology
cell morphology
@ref | gram stain | motility | confidence |
---|---|---|---|
32184 | positive | no | |
69480 | positive | 100 |
pigmentation
- @ref: 32184
- production: yes
multimedia
- @ref: 12253
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45023.jpg
- caption: Medium 65 28°C pH 9.5
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
12253 | GYP GLUCOSE-YEAST-PEPTONE MEDIUM (DSMZ Medium 852) | yes | https://mediadive.dsmz.de/medium/852 | Name: GYP GLUCOSE-YEAST-PEPTONE MEDIUM (DSMZ Medium 852) Composition: Glucose 20.0 g/l Yeast extract 10.0 g/l Peptone 10.0 g/l Na-acetate 10.0 g/l Agar 10.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x 4 H2O 0.01 g/l FeSO4 x 7 H2O 0.01 g/l NaCl 0.01 g/l Distilled water |
12253 | BOGORIELLA MEDIUM (DSMZ Medium 785) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium785.pdf |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
12253 | positive | growth | 28 | mesophilic |
32184 | positive | optimum | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32184 | positive | growth | 08-14 | alkaliphile |
32184 | positive | optimum | 9.5-13 |
Physiology and metabolism
oxygen tolerance
- @ref: 32184
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
32184 | yes | |
69481 | yes | 100 |
69480 | yes | 99.191 |
halophily
- @ref: 32184
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-5 %
observation
- @ref: 67770
- observation: quinones: MK-10(H2), MK-10(H4), MK-10(H6)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32184 | 22599 | arabinose | + | carbon source |
32184 | 17754 | glycerol | + | carbon source |
32184 | 17716 | lactose | + | carbon source |
32184 | 18222 | xylose | + | carbon source |
32184 | 17632 | nitrate | + | reduction |
enzymes
- @ref: 32184
- value: gelatinase
- activity: +
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
12253 | soil of saline | Buerjin of Xinjiang Province | China | CHN | Asia |
67770 | Soil from an alkali lake | Xinjiang | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Soil |
#Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_7141.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_1213;99_7141&stattab=map
- Last taxonomy: Nocardiopsis
- 16S sequence: AY336503
- Sequence Identity:
- Total samples: 26
- soil counts: 2
- aquatic counts: 1
- animal counts: 23
Safety information
risk assessment
- @ref: 12253
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 12253
- description: Nocardiopsis valliformis strain HBUM 20028 16S ribosomal RNA gene, partial sequence
- accession: AY336503
- length: 1434
- database: ena
- NCBI tax ID: 239974
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nocardiopsis valliformis DSM 45023 | 1246448.3 | wgs | patric | 1246448 |
66792 | Nocardiopsis valliformis DSM 45023 | 2554235029 | draft | img | 1246448 |
67770 | Nocardiopsis valliformis DSM 45023 | GCA_000340985 | contig | ncbi | 1246448 |
GC content
@ref | GC-content | method |
---|---|---|
12253 | 70.6 | high performance liquid chromatography (HPLC) |
32184 | 70.6 | |
67770 | 69.6 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 93.242 | yes |
gram-positive | yes | 93.516 | no |
anaerobic | no | 99.318 | yes |
aerobic | yes | 94.72 | yes |
halophile | yes | 56.391 | no |
spore-forming | yes | 91.634 | yes |
glucose-util | yes | 88.491 | no |
flagellated | no | 97.77 | yes |
thermophile | no | 98.27 | yes |
glucose-ferment | no | 92.467 | no |
External links
@ref: 12253
culture collection no.: DSM 45023, CGMCC 4.2135, HBUM 20028, JCM 16800
straininfo link
- @ref: 80470
- straininfo: 297493
literature
- topic: Phylogeny
- Pubmed-ID: 18599691
- title: Nocardiopsis valliformis sp. nov., an alkaliphilic actinomycete isolated from alkali lake soil in China.
- authors: Yang R, Zhang LP, Guo LG, Shi N, Lu Z, Zhang X
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.65090-0
- year: 2008
- mesh: Actinomycetales/*classification/genetics/*isolation & purification/ultrastructure, *Alkalies, China, *Fresh Water, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
12253 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45023) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45023 | |||
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 | |||
32184 | 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 | 28426 | 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) | |||
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 | |||
80470 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297493.1 | StrainInfo: A central database for resolving microbial strain identifiers |