Strain identifier
BacDive ID: 17412
Type strain:
Species: Labrys miyagiensis
Strain Designation: G24103
Strain history: CIP <- 2007, NCIMB
NCBI tax ID(s): 346912 (species)
General
@ref: 7365
BacDive-ID: 17412
DSM-Number: 18384
keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Labrys miyagiensis G24103 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from grassland soil.
NCBI tax id
- NCBI tax id: 346912
- Matching level: species
strain history
@ref | history |
---|---|
7365 | <- H. Kawasaki; G24103 <- T. Hattori |
34353 | 2007, NCIMB |
36798 | 2007, NCIMB |
120981 | CIP <- 2007, NCIMB |
doi: 10.13145/bacdive17412.20230509.8.1
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 miyagiensis
- full scientific name: Labrys miyagiensis Islam et al. 2007
@ref: 7365
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Xanthobacteraceae
genus: Labrys
species: Labrys miyagiensis
full scientific name: Labrys miyagiensis Islam et al. 2007
strain designation: G24103
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility |
---|---|---|---|
31771 | negative | rod-shaped | yes |
120981 | negative | rod-shaped | no |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7365 | YM MEDIUM (DSMZ Medium 1070) | yes | https://mediadive.dsmz.de/medium/1070 | Name: YM MEDIUM (DSMZ Medium 1070) Composition: Mannitol 10.0 g/l K2HPO4 0.5 g/l Yeast extract 0.5 g/l CaCl2 x 2 H2O 0.2 g/l NaCl 0.2 g/l MgSO4 x 7 H2O 0.1 g/l Distilled water |
34353 | MEDIUM 694 - for Labrys | yes | ||
36798 | MEDIUM 694 - for Labrys | yes | ||
120981 | CIP Medium 694 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=694 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7365 | positive | growth | 28 | mesophilic |
31771 | positive | growth | 15-32 | |
31771 | positive | optimum | 23.5 | psychrophilic |
34353 | positive | growth | 25 | mesophilic |
36798 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31771 | positive | growth | 4.0-9.0 | alkaliphile |
31771 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31771 | aerobe |
120981 | obligate aerobe |
spore formation
- @ref: 31771
- spore formation: no
halophily
- @ref: 31771
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <0.3 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31771 | 15963 | ribitol | + | carbon source |
31771 | 22599 | arabinose | + | carbon source |
31771 | 29016 | arginine | + | carbon source |
31771 | 17057 | cellobiose | + | carbon source |
31771 | 28757 | fructose | + | carbon source |
31771 | 28260 | galactose | + | carbon source |
31771 | 17234 | glucose | + | carbon source |
31771 | 27570 | histidine | + | carbon source |
31771 | 17306 | maltose | + | carbon source |
31771 | 29864 | mannitol | + | carbon source |
31771 | 26271 | proline | + | carbon source |
31771 | 26546 | rhamnose | + | carbon source |
31771 | 17822 | serine | + | carbon source |
31771 | 30911 | sorbitol | + | carbon source |
31771 | 17992 | sucrose | + | carbon source |
31771 | 26986 | threonine | + | carbon source |
31771 | 27082 | trehalose | + | carbon source |
31771 | 16296 | D-tryptophan | + | carbon source |
31771 | 17151 | xylitol | + | carbon source |
31771 | 18222 | xylose | + | carbon source |
120981 | 17632 | nitrate | - | reduction |
120981 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 120981
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
31771 | catalase | + | 1.11.1.6 |
31771 | cytochrome oxidase | + | 1.9.3.1 |
120981 | oxidase | + | |
120981 | catalase | + | 1.11.1.6 |
120981 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120981 | - | + | + | + | - | + | - | - | + | - | + | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7365 | grassland soil | Miyagi, Sendai | Japan | JPN | Asia |
120981 | Environment, Soil, grassland | Sendai, Miyagi | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Grassland |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_58597.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_116;97_123;98_138;99_58597&stattab=map
- Last taxonomy: Labrys miyagiensis
- 16S sequence: AB681464
- Sequence Identity:
- Total samples: 56
- soil counts: 45
- aquatic counts: 2
- animal counts: 5
- plant counts: 4
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7365 | 1 | Risk group (German classification) |
120981 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Labrys miyagiensis gene for 16S rRNA, partial sequence, strain: NBRC 101365 | AB681464 | 1412 | ena | 346912 |
7365 | Labrys miyagiensis gene for 16S rRNA, partial sequence, strain: G24103 | AB236170 | 1409 | ena | 346912 |
GC content
@ref | GC-content |
---|---|
7365 | 61.4 |
31771 | 65 |
External links
@ref: 7365
culture collection no.: DSM 18384, NBRC 101365, NCIMB 14143, CIP 109578
straininfo link
- @ref: 86408
- straininfo: 297244
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
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 | 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 |
Phylogeny | 28875912 | Labrys soli sp. nov., isolated from the rhizosphere of ginseng. | Nguyen NL, Kim YJ, Hoang VA, Kang JP, Wang C, Zhang J, Kang CH, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000512 | 2015 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
7365 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18384) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18384 | ||||
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 | ||
31771 | 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 | 28044 | ||
34353 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7338 | |||||
36798 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7337 | |||||
68382 | Automatically annotated from API zym | ||||||
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 | ||||
86408 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297244.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
120981 | Curators of the CIP | Collection of Institut Pasteur (CIP 109578) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109578 |