Strain identifier
BacDive ID: 17410
Type strain: 
Species: Labrys methylaminiphila
Strain Designation: JLW10
Strain history: IAM 15351 <-- DSM 16812 <-- M. G. Kalyuzhnaya <-- J. A. Miller et al. JLW10.
NCBI tax ID(s): 1096091 (strain), 298598 (species)
version 8.1 (current version)
General
@ref: 6611
BacDive-ID: 17410
DSM-Number: 16812
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Labrys methylaminiphila JLW10 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Lake washington sediment.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1096091 | strain |
| 298598 | species |
strain history
| @ref | history |
|---|---|
| 6611 | <- M. G. Kalyuzhnaya <- J. A. Miller et al.; JLW10 |
| 67770 | IAM 15351 <-- DSM 16812 <-- M. G. Kalyuzhnaya <-- J. A. Miller et al. JLW10. |
doi: 10.13145/bacdive17410.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Xanthobacteraceae
- genus: Labrys
- species: Labrys methylaminiphila
- full scientific name: Labrys methylaminiphila corrig. Miller et al. 2005
synonyms
- @ref: 20215
- synonym: Labrys methylaminiphilus
@ref: 6611
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Xanthobacteraceae
genus: Labrys
species: Labrys methylaminiphilus
full scientific name: Labrys methylaminiphilus Miller et al. 2005
strain designation: JLW10
type strain: yes
Morphology
cell morphology
- @ref: 31365
- gram stain: negative
- cell length: 1.1 µm
- cell width: 0.85 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 31365
- production: no
Culture and growth conditions
culture medium
- @ref: 6611
- name: MINERAL MEDIUM PH 7.25 (DSMZ Medium 465)
- growth: yes
- link: https://mediadive.dsmz.de/medium/465
- composition: Name: MINERAL MEDIUM PH 7.25 (DSMZ Medium 465; with strain-specific modifications) Composition: Na2HPO4 x 2 H2O 3.5 g/l KH2PO4 1.0 g/l (NH4)2SO4 0.5 g/l MgCl2 x 6 H2O 0.1 g/l Ca(NO3)2 x 4 H2O 0.05 g/l Na2-EDTA 0.0005 g/l H3BO3 0.0003 g/l FeSO4 x 7 H2O 0.0002 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l None Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 6611 | positive | growth | 28 | mesophilic |
| 31365 | positive | growth | 10-35 | |
| 31365 | positive | optimum | 29 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31365 | positive | growth | 4-9.5 | alkaliphile |
| 31365 | positive | optimum | 6 |
Physiology and metabolism
oxygen tolerance
- @ref: 31365
- oxygen tolerance: aerobe
spore formation
- @ref: 31365
- spore formation: no
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31365 | 17822 | serine | + | carbon source |
| 31365 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31365 | catalase | + | 1.11.1.6 |
| 31365 | gelatinase | + | |
| 31365 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 6611 | Lake washington sediment | Washington | USA | USA | North America |
| 67770 | Sediment of Lake Washington | Seattle, WA | USA | USA | North America |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Aquatic | #Sediment |
Safety information
risk assessment
- @ref: 6611
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Labrys methylaminiphilus gene for 16S rRNA, partial sequence, strain: DSM 16812 | AB236172 | 1409 | ena | 1096091 |
| 6611 | Labrys methylaminiphilus 16S ribosomal RNA gene, partial sequence | AY766152 | 1405 | ena | 1096091 |
Genome sequences
- @ref: 66792
- description: Labrys methylaminiphilus JLW10
- accession: 2565956506
- assembly level: draft
- database: img
- NCBI tax ID: 1096091
GC content
| @ref | GC-content | method |
|---|---|---|
| 6611 | 65.7 | |
| 67770 | 65.4-66 | high performance liquid chromatography (HPLC) |
External links
@ref: 6611
culture collection no.: DSM 16812, ATCC BAA 1080, JCM 21796, IAM 15351
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15879264 | Labrys methylaminiphilus sp. nov., a novel facultatively methylotrophic bacterium from a freshwater lake sediment. | Miller JA, Kalyuzhnaya MG, Noyes E, Lara JC, Lidstrom ME, Chistoserdova L | Int J Syst Evol Microbiol | 10.1099/ijs.0.63409-0 | 2005 | Alcohols/metabolism, Alphaproteobacteria/*classification/cytology/*isolation & purification/physiology, Amino Acids/metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Carboxylic Acids/metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Fresh Water/*microbiology, Genes, rRNA, Gentian Violet, Geologic Sediments/*microbiology, Hydrocarbons, Aromatic/metabolism, Methylamines/*metabolism, Molecular Sequence Data, Phenazines, Phospholipids/analysis/isolation & purification, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Water Microbiology | Metabolism |
| Phylogeny | 17329783 | Labrys okinawensis sp. nov. and Labrys miyagiensis sp. nov., budding bacteria isolated from rhizosphere habitats in Japan, and emended descriptions of the genus Labrys and Labrys monachus. | Islam MS, Kawasaki H, Nakagawa Y, Hattori T, Seki T | Int J Syst Evol Microbiol | 10.1099/ijs.0.64239-0 | 2007 | Alphaproteobacteria/chemistry/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Japan, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology | Genetics |
| Phylogeny | 17329788 | Labrys neptuniae sp. nov., isolated from root nodules of the aquatic legume Neptunia oleracea. | Chou YJ, Elliott GN, James EK, Lin KY, Chou JH, Sheu SY, Sheu DS, Sprent JI, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.64553-0 | 2007 | Alphaproteobacteria/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fabaceae/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Taiwan | Genetics |
| Phylogeny | 19684322 | Labrys wisconsinensis sp. nov., a budding bacterium isolated from Lake Michigan water, and emended description of the genus Labrys. | Albert RA, Waas NE, Langer S, Pavlons SC, Feldner JL, Rossello-Mora R, Busse HJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.014977-0 | 2009 | Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, Base Sequence, Fresh Water/*microbiology, Lipids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
|---|---|---|---|---|---|---|---|
| 6611 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16812) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16812 | ||||
| 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 | ||
| 31365 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 27678 | ||
| 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/ |