Strain identifier

BacDive ID: 17412

Type strain: Yes

Species: Labrys miyagiensis

Strain Designation: G24103

Strain history: CIP <- 2007, NCIMB

NCBI tax ID(s): 346912 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
7365<- H. Kawasaki; G24103 <- T. Hattori
343532007, NCIMB
367982007, NCIMB
120981CIP <- 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

@refgram staincell shapemotility
31771negativerod-shapedyes
120981negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7365YM MEDIUM (DSMZ Medium 1070)yeshttps://mediadive.dsmz.de/medium/1070Name: 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
34353MEDIUM 694 - for Labrysyes
36798MEDIUM 694 - for Labrysyes
120981CIP Medium 694yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=694

culture temp

@refgrowthtypetemperaturerange
7365positivegrowth28mesophilic
31771positivegrowth15-32
31771positiveoptimum23.5psychrophilic
34353positivegrowth25mesophilic
36798positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
31771positivegrowth4.0-9.0alkaliphile
31771positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31771aerobe
120981obligate aerobe

spore formation

  • @ref: 31771
  • spore formation: no

halophily

  • @ref: 31771
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <0.3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3177115963ribitol+carbon source
3177122599arabinose+carbon source
3177129016arginine+carbon source
3177117057cellobiose+carbon source
3177128757fructose+carbon source
3177128260galactose+carbon source
3177117234glucose+carbon source
3177127570histidine+carbon source
3177117306maltose+carbon source
3177129864mannitol+carbon source
3177126271proline+carbon source
3177126546rhamnose+carbon source
3177117822serine+carbon source
3177130911sorbitol+carbon source
3177117992sucrose+carbon source
3177126986threonine+carbon source
3177127082trehalose+carbon source
3177116296D-tryptophan+carbon source
3177117151xylitol+carbon source
3177118222xylose+carbon source
12098117632nitrate-reduction
12098116301nitrite-reduction

metabolite production

  • @ref: 120981
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31771catalase+1.11.1.6
31771cytochrome oxidase+1.9.3.1
120981oxidase+
120981catalase+1.11.1.6
120981urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120981-+++-+--+-++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7365grassland soilMiyagi, SendaiJapanJPNAsia
120981Environment, Soil, grasslandSendai, MiyagiJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
73651Risk group (German classification)
1209811Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Labrys miyagiensis gene for 16S rRNA, partial sequence, strain: NBRC 101365AB6814641412ena346912
7365Labrys miyagiensis gene for 16S rRNA, partial sequence, strain: G24103AB2361701409ena346912

GC content

@refGC-content
736561.4
3177165

External links

@ref: 7365

culture collection no.: DSM 18384, NBRC 101365, NCIMB 14143, CIP 109578

straininfo link

  • @ref: 86408
  • straininfo: 297244

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17329783Labrys 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 TInt J Syst Evol Microbiol10.1099/ijs.0.64239-02007Alphaproteobacteria/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 MicrobiologyGenetics
Phylogeny19684322Labrys 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 HJInt J Syst Evol Microbiol10.1099/ijs.0.014977-02009Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, Base Sequence, Fresh Water/*microbiology, Lipids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny28875912Labrys soli sp. nov., isolated from the rhizosphere of ginseng.Nguyen NL, Kim YJ, Hoang VA, Kang JP, Wang C, Zhang J, Kang CH, Yang DCInt J Syst Evol Microbiol10.1099/ijsem.0.0005122015

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7365Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18384)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18384
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31771Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128044
34353Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7338
36798Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7337
68382Automatically annotated from API zym
69479João 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
86408Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297244.1StrainInfo: A central database for resolving microbial strain identifiers
120981Curators of the CIPCollection of Institut Pasteur (CIP 109578)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109578