Strain identifier
BacDive ID: 5978
Type strain: 
Species: Acetohalobium arabaticum
Strain Designation: Z-7288
Strain history: <- T.N. Zhilina, Z-7288
NCBI tax ID(s): 574087 (strain), 28187 (species)
version 8.1 (current version)
General
@ref: 2083
BacDive-ID: 5978
DSM-Number: 5501
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-negative
description: Acetohalobium arabaticum Z-7288 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from lagoons.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 28187 | species |
| 574087 | strain |
strain history
- @ref: 2083
- history: <- T.N. Zhilina, Z-7288
doi: 10.13145/bacdive5978.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Halanaerobiales
- family: Halobacteroidaceae
- genus: Acetohalobium
- species: Acetohalobium arabaticum
- full scientific name: Acetohalobium arabaticum Zhilina and Zavarzin 1990
@ref: 2083
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Halanaerobiales
family: Halobacteroidaceae
genus: Acetohalobium
species: Acetohalobium arabaticum
full scientific name: Acetohalobium arabaticum Zhilina and Zavarzin 1990
strain designation: Z-7288
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 98.498
colony morphology
- @ref: 2083
- incubation period: 3-7 days
multimedia
- @ref: 66793
- multimedia content: EM_DSM_5501_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 2083
- name: ACETOHALOBIUM MEDIUM (DSMZ Medium 494)
- growth: yes
- link: https://mediadive.dsmz.de/medium/494
- composition: Name: ACETOHALOBIUM MEDIUM (DSMZ Medium 494) Composition: MgCl2 x 6 H2O 3.95648 g/l Trimethylamine-HCl 2.37389 g/l Na2CO3 1.97824 g/l Na2S x 9 H2O 0.49456 g/l KCl 0.326409 g/l NH4Cl 0.326409 g/l KH2PO4 0.326409 g/l Yeast extract 0.049456 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l CuSO4 x 5 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Biotin 1.97824e-05 g/l Folic acid 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water
culture temp
- @ref: 2083
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 2083 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 99.446 |
Isolation, sampling and environmental information
isolation
- @ref: 2083
- sample type: lagoons
- geographic location: East Crimea, Arabat spit
- country: Russia
- origin.country: RUS
- continent: Europe
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
taxonmaps
- @ref: 69479
- File name: preview.99_1928.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_270;96_1079;97_1259;98_1513;99_1928&stattab=map
- Last taxonomy: Acetohalobium arabaticum subclade
- 16S sequence: X89077
- Sequence Identity:
- Total samples: 3021
- soil counts: 121
- aquatic counts: 183
- animal counts: 2676
- plant counts: 41
Safety information
risk assessment
- @ref: 2083
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Acetohalobium arabaticum 16S ribosomal RNA gene, complete sequence | L37422 | 1475 | ena | 574087 |
| 2083 | H.arabaticum gene for 16S ribosomal RNA | X89077 | 1472 | ena | 574087 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Acetohalobium arabaticum DSM 5501 | GCA_000144695 | complete | ncbi | 574087 |
| 66792 | Acetohalobium arabaticum DSM 5501 | 574087.3 | complete | patric | 574087 |
| 66792 | Acetohalobium arabaticum Z-7288, DSM 5501 | 648028002 | complete | img | 574087 |
GC content
- @ref: 2083
- GC-content: 33.6
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 85.779 | no |
| flagellated | no | 72.721 | no |
| gram-positive | no | 96.197 | no |
| anaerobic | yes | 99.287 | yes |
| aerobic | no | 97.045 | yes |
| halophile | no | 65.991 | no |
| spore-forming | yes | 57.129 | no |
| thermophile | yes | 79.383 | no |
| glucose-util | yes | 70.512 | no |
| glucose-ferment | no | 72.578 | no |
External links
@ref: 2083
culture collection no.: DSM 5501, ATCC 49924
straininfo link
- @ref: 75467
- straininfo: 42757
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh |
|---|---|---|---|---|---|---|---|
| Genetics | 21304692 | Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288). | Sikorski J, Lapidus A, Chertkov O, Lucas S, Copeland A, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Han C, Brambilla E, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Bruce D, Detter C, Tapia R, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Goker M, Spring S, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP | Stand Genomic Sci | 10.4056/sigs.1062906 | 2010 | |
| Metabolism | 34908470 | Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance. | Tirumalai MR, Anane-Bediakoh D, Rajesh S, Fox GE | Microbiol Spectr | 10.1128/spectrum.01782-21 | 2021 | Archaea/genetics/*metabolism, Bacterial Proteins/genetics, Bacteroidetes/genetics/*metabolism, Eukaryota/genetics/*metabolism, Firmicutes/genetics/*metabolism, Halobacteriales/genetics, Ribosomal Proteins/*chemistry, Ribosomes/chemistry, Sodium Chloride/*metabolism, Static Electricity |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 2083 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5501) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5501 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 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 | |||
| 75467 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42757.1 | StrainInfo: A central database for resolving microbial strain identifiers |