Strain identifier
BacDive ID: 32
Type strain: 
Species: Acidocella aminolytica
Strain history: N. Kishimoto 101.
NCBI tax ID(s): 1120923 (strain), 33998 (species)
version 9.3 (current version)
General
@ref: 4254
BacDive-ID: 32
DSM-Number: 11237
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Acidocella aminolytica DSM 11237 is a mesophilic, Gram-negative bacterium that was isolated from acidic mine drainage.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1120923 | strain |
| 33998 | species |
strain history
| @ref | history |
|---|---|
| 4254 | <- JCM <- N. Kishimoto, strain 101 (Acidiphilium aminolytica) |
| 67770 | N. Kishimoto 101. |
doi: 10.13145/bacdive32.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodospirillales
- family: Acetobacteraceae
- genus: Acidocella
- species: Acidocella aminolytica
- full scientific name: Acidocella aminolytica corrig. (Kishimoto et al. 1994) Kishimoto et al. 1996
synonyms
@ref synonym 20215 Acidiphilium aminilyticum 20215 Acidiphilium aminolytica
@ref: 4254
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Acetobacteraceae
genus: Acidocella
species: Acidocella aminolytica
full scientific name: Acidocella aminolytica (Kishimoto et al. 1994) Kishimoto et al. 1996
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 94.5 |
| 125439 | negative | 90.2 |
Culture and growth conditions
culture medium
- @ref: 4254
- name: ACIDIPHILIUM MEDIUM (DSMZ Medium 269)
- growth: yes
- link: https://mediadive.dsmz.de/medium/269
- composition: Name: ACIDIPHILIUM MEDIUM (DSMZ Medium 269; with strain-specific modifications) Composition: (NH4)2SO4 2.0 g/l D-Glucose 1.0 g/l MgSO4 x 7 H2O 0.5 g/l K2HPO4 0.5 g/l Yeast extract 0.1 g/l KCl 0.1 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 4254 | positive | growth | 37 |
| 67770 | positive | growth | 37 |
Physiology and metabolism
spore formation
- @ref: 125439
- spore formation: no
- confidence: 92.7
observation
- @ref: 67770
- observation: quinones: Q-10
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 4254 | acidic mine drainage | Okayama, Yanahara mine | Japan | JPN | Asia |
| 67770 | Acidic mine drainage |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Other | #Mine |
| #Environmental | #Aquatic | |
| #Condition | #Acidic |
taxonmaps
- @ref: 69479
- File name: preview.99_6639.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_3146;97_3854;98_4895;99_6639&stattab=map
- Last taxonomy: Acidocella aminolytica subclade
- 16S sequence: D30771
- Sequence Identity:
- Total samples: 1551
- soil counts: 754
- aquatic counts: 387
- animal counts: 159
- plant counts: 251
Safety information
risk assessment
- @ref: 4254
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4254
- description: Acidocella aminolytica gene for 16S ribosomal RNA
- accession: D30771
- length: 1406
- database: nuccore
- NCBI tax ID: 33998
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Acidocella aminolytica 101 = DSM 11237 | 1120923.5 | wgs | patric | 1120923 |
| 66792 | Acidocella aminolytica 101 = DSM 11237 | 1120923.7 | wgs | patric | 1120923 |
| 66792 | Acidocella aminolytica DSM 11237 | 2582581264 | draft | img | 1120923 |
| 67770 | Acidocella aminolytica 101 = DSM 11237 | GCA_000964385 | scaffold | ncbi | 1120923 |
| 67770 | Acidocella aminolytica 101 = DSM 11237 | GCA_900129125 | scaffold | ncbi | 1120923 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 4254 | 58.7 | |
| 67770 | 59.1 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | facultative aerobe | 71.3 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 90.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 50.5 | |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 92.7 | |
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 94.5 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 91.666 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 83.986 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 83.567 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 95.452 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 76.229 | no |
External links
@ref: 4254
culture collection no.: DSM 11237, ATCC 51361, JCM 8796
straininfo link
- @ref: 69716
- straininfo: 42948
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4254 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11237) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11237 | |||
| 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 | |
| 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 | |||
| 69716 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42948.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |