Strain identifier
BacDive ID: 2247
Type strain: 
Species: Alkalibacterium subtropicum
Strain Designation: 024-2
Strain history: <- M. Ishikawa and K. Yamasato, Tokyo University of Agriculture, Dept. of Applied Bio-Science; 024-2
NCBI tax ID(s): 753702 (species)
version 8.1 (current version)
General
@ref: 17332
BacDive-ID: 2247
DSM-Number: 23664
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive
description: Alkalibacterium subtropicum 024-2 is a mesophilic, Gram-positive bacterium that was isolated from decaying marine alga, Galaxaura sp..
NCBI tax id
- NCBI tax id: 753702
- Matching level: species
strain history
- @ref: 17332
- history: <- M. Ishikawa and K. Yamasato, Tokyo University of Agriculture, Dept. of Applied Bio-Science; 024-2
doi: 10.13145/bacdive2247.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Carnobacteriaceae
- genus: Alkalibacterium
- species: Alkalibacterium subtropicum
- full scientific name: Alkalibacterium subtropicum Ishikawa et al. 2011
@ref: 17332
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Carnobacteriaceae
genus: Alkalibacterium
species: Alkalibacterium subtropicum
full scientific name: Alkalibacterium subtropicum Ishikawa et al. 2011
strain designation: 024-2
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 17332
- name: BOGORIELLA MEDIUM (DSMZ Medium 785)
- growth: yes
- link: https://mediadive.dsmz.de/medium/785
- composition: Name: BOGORIELLA MEDIUM (DSMZ Medium 785) Composition: NaCl 40.0 g/l Glucose 10.0 g/l Na2CO3 10.0 g/l Yeast extract 5.0 g/l Peptone 5.0 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.2 g/l Distilled water
culture temp
- @ref: 17332
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 90 |
| 69480 | no | 99.931 |
murein
- @ref: 17332
- murein short key: A21.04
- type: A4ß L-Orn-D-Asp
Isolation, sampling and environmental information
isolation
- @ref: 17332
- sample type: decaying marine alga, Galaxaura sp.
- host species: Galaxaura
- geographic location: Okinawa Prefecture, Ouijima Islet, foreshore site
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Host | #Algae | #Red algae |
| #Host | #Plants | #Decomposing plant |
taxonmaps
- @ref: 69479
- File name: preview.99_79981.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_27;96_47;97_49;98_16554;99_79981&stattab=map
- Last taxonomy: Alkalibacterium
- 16S sequence: AB555562
- Sequence Identity:
- Total samples: 416
- soil counts: 21
- aquatic counts: 167
- animal counts: 226
- plant counts: 2
Safety information
risk assessment
- @ref: 17332
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17332
- description: Alkalibacterium subtropicum gene for 16S rRNA, partial sequence, strain: O24-2
- accession: AB555562
- length: 1507
- database: ena
- NCBI tax ID: 753702
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Alkalibacterium subtropicum DSM 23664 | GCA_900112455 | scaffold | ncbi | 753702 |
| 66792 | Alkalibacterium subtropicum strain DSM 23664 | 753702.4 | wgs | patric | 753702 |
| 66792 | Alkalibacterium subtropicum DSM 23664 | 2616644818 | draft | img | 753702 |
GC content
- @ref: 17332
- GC-content: 43.7
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 90 | no |
| motile | yes | 68.786 | no |
| flagellated | no | 83.295 | no |
| gram-positive | yes | 89.024 | no |
| anaerobic | no | 90.993 | no |
| aerobic | no | 90.404 | no |
| halophile | yes | 89.045 | no |
| spore-forming | no | 84.634 | no |
| glucose-ferment | yes | 76.841 | no |
| thermophile | no | 98.361 | yes |
| glucose-util | yes | 90.685 | no |
External links
@ref: 17332
culture collection no.: DSM 23664, NBRC 107172
straininfo link
- @ref: 71806
- straininfo: 402338
literature
- topic: Phylogeny
- Pubmed-ID: 21296925
- title: Alkalibacterium subtropicum sp. nov., a slightly halophilic and alkaliphilic marine lactic acid bacterium isolated from decaying marine algae.
- authors: Ishikawa M, Nakajima K, Ishizaki S, Kodama K, Okamoto-Kainuma A, Koizumi Y, Yamamoto Y, Yamasato K
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.027953-0
- year: 2011
- mesh: Alkalies/*metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Lactic Acid/*metabolism, Lactobacillales/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phaeophyta/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodophyta/*microbiology, Seawater/*microbiology, Sodium Chloride/*metabolism
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 17332 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23664) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23664 | |
| 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) | |
| 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 | |
| 71806 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402338.1 | StrainInfo: A central database for resolving microbial strain identifiers |