Strain identifier
BacDive ID: 18086
Type strain: 
Species: Natranaerovirga pectinivora
Strain Designation: AP3
Strain history: <- D. Y. Sorokin, Dept. Biotechnol., Delft Univ. Technol., Netherlands; AP3 <- D. Y. Sorokin {2010}
NCBI tax ID(s): 682400 (species)
version 8.1 (current version)
General
@ref: 17720
BacDive-ID: 18086
DSM-Number: 24629
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive
description: Natranaerovirga pectinivora AP3 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from soda solonchak soil.
NCBI tax id
- NCBI tax id: 682400
- Matching level: species
strain history
- @ref: 17720
- history: <- D. Y. Sorokin, Dept. Biotechnol., Delft Univ. Technol., Netherlands; AP3 <- D. Y. Sorokin {2010}
doi: 10.13145/bacdive18086.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Lachnospiraceae
- genus: Natranaerovirga
- species: Natranaerovirga pectinivora
- full scientific name: Natranaerovirga pectinivora Sorokin et al. 2012
@ref: 17720
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Lachnospiraceae
genus: Natranaerovirga
species: Natranaerovirga pectinivora
full scientific name: Natranaerovirga pectinivora Sorokin et al. 2012 emend. Schouw et al. 2016
strain designation: AP3
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 17720
- name: DESULFONATRONUM THIOAUTOTROPHICUM MEDIUM (DSMZ Medium 1166)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1166
- composition: Name: DESULFONATRONUM THIOAUTOTROPHICUM MEDIUM (DSMZ Medium 1166; with strain-specific modifications) Composition: Na2CO3 21.9342 g/l NaHCO3 7.97607 g/l NaCl 5.98205 g/l Na2S2O3 x 5 H2O 4.98504 g/l Na2SO4 2.79163 g/l K2HPO4 0.997009 g/l D-galacturonic acid 0.997009 g/l Na2S x 9 H2O 0.239282 g/l NH4Cl 0.199402 g/l MgCl2 x 6 H2O 0.199402 g/l Yeast extract 0.0498504 g/l EDTA 0.00498504 g/l FeSO4 x 7 H2O 0.00219342 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000199402 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnSO4 x 7 H2O 9.97009e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l MnCl2 x 4 H2O 2.99103e-05 g/l NiCl2 x 6 H2O 2.99103e-05 g/l Na2MoO4 x 2 H2O 2.99103e-05 g/l CuCl2 x 2 H2O 2.99103e-05 g/l H3BO3 2.99103e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water
culture temp
- @ref: 17720
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 17720 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 91 |
| 69480 | yes | 99.154 |
Isolation, sampling and environmental information
isolation
- @ref: 17720
- sample type: soda solonchak soil
- geographic location: Southeast Siberia, Altai
- country: Russia
- origin.country: RUS
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Condition | #Alkaline |
taxonmaps
- @ref: 69479
- File name: preview.99_173906.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_922;96_48757;97_62713;98_83495;99_173906&stattab=map
- Last taxonomy: Natranaerovirga pectinivora subclade
- 16S sequence: GQ922846
- Sequence Identity:
- Total samples: 396
- soil counts: 12
- aquatic counts: 42
- animal counts: 341
- plant counts: 1
Safety information
risk assessment
- @ref: 17720
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17720
- description: Natranaerovirga pectinivora strain AP3 16S ribosomal RNA gene, partial sequence
- accession: GQ922846
- length: 1497
- database: ena
- NCBI tax ID: 682400
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Natranaerovirga pectinivora DSM 24629 | GCA_004342165 | scaffold | ncbi | 682400 |
| 66792 | Natranaerovirga pectinivora strain DSM 24629 | 682400.3 | wgs | patric | 682400 |
| 66792 | Natranaerovirga pectinivora DSM 24629 | 2784746802 | draft | img | 682400 |
GC content
- @ref: 17720
- GC-content: 30.7
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 91 | no |
| motile | yes | 85.676 | no |
| flagellated | yes | 57.705 | no |
| gram-positive | yes | 81.666 | no |
| anaerobic | yes | 99.254 | yes |
| aerobic | no | 98.663 | yes |
| halophile | no | 76.332 | no |
| spore-forming | yes | 90.4 | no |
| glucose-util | yes | 83.611 | no |
| thermophile | no | 98.457 | yes |
| glucose-ferment | yes | 57.176 | no |
External links
@ref: 17720
culture collection no.: DSM 24629, UNIQEM U805
straininfo link
- @ref: 87074
- straininfo: 406299
literature
- topic: Phylogeny
- Pubmed-ID: 22294481
- title: Anaerobic utilization of pectinous substrates at extremely haloalkaline conditions by Natranaerovirga pectinivora gen. nov., sp. nov., and Natranaerovirga hydrolytica sp. nov., isolated from hypersaline soda lakes.
- authors: Sorokin DY, Tourova TP, Panteleeva AN, Kaparullina EN, Muyzer G
- journal: Extremophiles
- DOI: 10.1007/s00792-012-0431-6
- year: 2012
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 17720 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24629) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24629 | |||
| 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 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 87074 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID406299.1 | StrainInfo: A central database for resolving microbial strain identifiers |