Strain identifier
BacDive ID: 1550
Type strain: 
Species: Salimicrobium halophilum
Strain Designation: N32-2
Strain history: DSM 4771 <-- A. Ventosa <-- M. Kamekura N23-2.
NCBI tax ID(s): 86666 (species)
version 9.1 (current version)
General
@ref: 1817
BacDive-ID: 1550
DSM-Number: 4771
keywords: genome sequence, 16S sequence, Bacteria, Gram-positive
description: Salimicrobium halophilum N32-2 is a Gram-positive bacterium that was isolated from rotting wood.
NCBI tax id
- NCBI tax id: 86666
- Matching level: species
strain history
| @ref | history |
|---|---|
| 1817 | <- A. Ventosa <- M. Kamekura, N32-2 |
| 67770 | DSM 4771 <-- A. Ventosa <-- M. Kamekura N23-2. |
doi: 10.13145/bacdive1550.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Salimicrobium
- species: Salimicrobium halophilum
- full scientific name: Salimicrobium halophilum (Ventosa et al. 1990) Yoon et al. 2007
synonyms
- @ref: 20215
- synonym: Bacillus halophilus
@ref: 1817
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Salimicrobium
species: Salimicrobium halophilum
full scientific name: Salimicrobium halophilum (Ventosa et al. 1990) Yoon et al. 2007
strain designation: N32-2
type strain: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 1817 | MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b) | yes | https://mediadive.dsmz.de/medium/514b | Name: MEDIUM 514 plus additional salt (DSMZ Medium 514b) Composition: NaCl 19.45 g/l Agar 17.5 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water |
| 1817 | 15% MH MEDIUM (DSMZ Medium 582) | yes | https://mediadive.dsmz.de/medium/582 | Name: 15% MH MEDIUM (DSMZ Medium 582) Composition: NaCl 121.5 g/l MgSO4 14.4 g/l MgCl2 10.5 g/l Yeast extract 10.0 g/l Proteose peptone no. 3 5.0 g/l KCl 3.0 g/l Glucose 1.0 g/l CaCl2 0.54 g/l NaHCO3 0.09 g/l NaBr 0.039 g/l Distilled water |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 1817 | positive | growth | 28 |
| 1817 | positive | growth | 37 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: MK-7
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 1817 | rotting wood | Seashore | Japan | JPN | Asia |
| 67770 | Rotting wood on the seashore in Nauru |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host Body Product | #Plant | #Timber |
| #Host | #Plants | #Tree |
| #Host | #Plants | #Decomposing plant |
taxonmaps
- @ref: 69479
- File name: preview.99_60011.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1295;97_1539;98_1873;99_60011&stattab=map
- Last taxonomy: Salimicrobium
- 16S sequence: AJ243920
- Sequence Identity:
- Total samples: 104
- soil counts: 9
- aquatic counts: 49
- animal counts: 45
- plant counts: 1
Safety information
risk assessment
- @ref: 1817
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Bacillus halophilus gene for 16S ribosomal RNA | AB021188 | 1517 | nuccore | 86666 |
| 20218 | Bacillus halophilus 16S rRNA gene, strain DSM 4771T | AJ243920 | 1425 | nuccore | 86666 |
| 20218 | Salimicrobium halophilum gene for 16S rRNA, partial sequence, strain: NBRC 102426 | AB681782 | 1493 | nuccore | 86666 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Salimicrobium halophilum strain DSM 4771 | 86666.3 | wgs | patric | 86666 |
| 66792 | Salimicrobium halophilum DSM 4771 | 2636416074 | draft | img | 86666 |
| 67770 | Salimicrobium halophilum DSM 4771 | GCA_900100295 | scaffold | ncbi | 86666 |
GC content
- @ref: 1817
- GC-content: 51.5
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 89 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 82.989 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.28 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 79.353 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 79.68 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 90.375 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 83.487 | no |
External links
@ref: 1817
culture collection no.: DSM 4771, ATCC 49085, CCM 4074, HAMBI 2106, JCM 12305, LMG 17942, IAM 14939, NBRC 102426
straininfo link
- @ref: 71195
- straininfo: 10533
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21596507 | Salimicrobium salexigens sp. nov., a moderately halophilic bacterium from salted hides. | de la Haba RR, Yilmaz P, Sanchez-Porro C, Birbir M, Ventosa A | Syst Appl Microbiol | 10.1016/j.syapm.2011.04.002 | 2011 | Animals, Animals, Domestic/microbiology, Australia, Bacillaceae/*classification/genetics, Base Sequence, DNA, Bacterial, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/chemistry/genetics, Skin/*microbiology | Genetics |
| Phylogeny | 25070217 | Salimicrobium jeotgali sp. nov., isolated from salted, fermented seafood. | Choi EJ, Jin HM, Kim KH, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.062042-0 | 2014 | Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Fermentation, *Food Microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seafood/*microbiology, Sequence Analysis, DNA, Sodium Chloride, Vitamin K 2/analogs & derivatives/chemistry | Biotechnology |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1817 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4771) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4771 | |||
| 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) | |||
| 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 | |||
| 71195 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID10533.1 | StrainInfo: A central database for resolving microbial strain identifiers |