Strain identifier
BacDive ID: 158081
Type strain: 
Species: Methylosinus sp.
Strain Designation: LW4
Strain history: <- A. Vorobev, Univ. of Washington, Dept. of Chemical Eng., Seattle, USA; LW4 <- M. G. Kalyuzhnaya <- A. J. Auman
NCBI tax ID(s): 427 (species)
version 9.3 (current version)
General
@ref: 64655
BacDive-ID: 158081
DSM-Number: 24479
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Methylosinus sp. LW4 is a mesophilic, Gram-negative bacterium that was isolated from Sediment.
NCBI tax id
- NCBI tax id: 427
- Matching level: species
strain history
- @ref: 64655
- history: <- A. Vorobev, Univ. of Washington, Dept. of Chemical Eng., Seattle, USA; LW4 <- M. G. Kalyuzhnaya <- A. J. Auman
doi: 10.13145/bacdive158081.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Methylocystaceae
- genus: Methylosinus
- species: Methylosinus sp.
- full scientific name: Methylosinus (ex Whittenbury et al. 1970) Bowman et al. 1993
@ref: 64655
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylocystaceae
genus: Methylosinus
species: Methylosinus sp.
full scientific name: Methylosinus sp.
strain designation: LW4
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 97.167 |
| 125439 | negative | 97.3 |
Culture and growth conditions
culture medium
- @ref: 64655
- name: MINERAL MEDIUM (DSMZ Medium 1007)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1007
- composition: Name: MINERAL MEDIUM (DSMZ Medium 1007) Composition: KNO3 0.25 g/l KH2PO4 0.1 g/l MgSO4 x 7 H2O 0.05 g/l CaCl2 x 2 H2O 0.01 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l CoCl2 x 6 H2O 0.0002 g/l CuCl2 x 5 H2O 0.0001 g/l ZnSO4 x 7 H2O 0.0001 g/l Na2MoO4 3e-05 g/l MnCl2 x 4 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l Distilled water
culture temp
- @ref: 64655
- growth: positive
- type: growth
- temperature: 25
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 96.7
spore formation
- @ref: 125439
- spore formation: no
- confidence: 92.7
Isolation, sampling and environmental information
isolation
- @ref: 64655
- sample type: Sediment
- geographic location: Washington Lake
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Terrestrial | #Sediment |
Sequence information
16S sequences
- @ref: 64655
- description: Methylosinus sp. LW4 16S ribosomal RNA gene, partial sequence
- accession: AY007293
- length: 1448
- database: nuccore
- NCBI tax ID: 136993
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methylosinus sp. LW4 | GCA_000379125 | scaffold | ncbi | 136993 |
| 66792 | Methylosinus sp. LW4 | 136993.3 | wgs | patric | 136993 |
| 66792 | Methylosinus sp. LW4 | 2516493024 | draft | img | 136993 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.167 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 87.634 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 75.005 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.221 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.124 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 66.625 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 92.7 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 55.3 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 97.3 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 96.7 |
External links
@ref: 64655
culture collection no.: DSM 24479
straininfo link
- @ref: 110924
- straininfo: 406919
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 64655 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24479 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24479) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 110924 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID406919.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |