Strain identifier

BacDive ID: 13905

Type strain: Yes

Species: Shinella yambaruensis

Strain Designation: MS-4

Strain history: <- T. Matsui, Center of Molecular Biosciences, University of the Ryukyus; MS-4

NCBI tax ID(s): 415996 (species)

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General

@ref: 7706

BacDive-ID: 13905

DSM-Number: 18801

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped

description: Shinella yambaruensis MS-4 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 415996
  • Matching level: species

strain history

  • @ref: 7706
  • history: <- T. Matsui, Center of Molecular Biosciences, University of the Ryukyus; MS-4

doi: 10.13145/bacdive13905.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Shinella
  • species: Shinella yambaruensis
  • full scientific name: Shinella yambaruensis Matsui et al. 2009

@ref: 7706

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Shinella

species: Shinella yambaruensis

full scientific name: Shinella yambaruensis Matsui et al. 2009

strain designation: MS-4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32445negative1.6-2.1 µm1.0-1.2 µmrod-shapedno
69480negative98.5

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7706NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Glucose 10.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
7706R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperature
7706positivegrowth28
32445positivegrowth15-42
32445positiveoptimum28.5

culture pH

@refabilitytypepHPH range
32445positivegrowth4-9alkaliphile
32445positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32445
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32445no
69480no93.236

halophily

@refsaltgrowthtested relationconcentration
32445NaClpositivegrowth0-2 %
32445NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3244515963ribitol+carbon source
3244522599arabinose+carbon source
3244518403L-arabitol+carbon source
3244517057cellobiose+carbon source
3244528757fructose+carbon source
3244533984fucose+carbon source
3244528260galactose+carbon source
3244517234glucose+carbon source
3244517754glycerol+carbon source
3244517306maltose+carbon source
3244529864mannitol+carbon source
3244537684mannose+carbon source
3244526546rhamnose+carbon source
3244533942ribose+carbon source
3244530911sorbitol+carbon source
3244517992sucrose+carbon source
3244527082trehalose+carbon source
3244517151xylitol+carbon source
3244518222xylose+carbon source
324454853esculin+hydrolysis

enzymes

@refvalueactivityec
32445catalase+1.11.1.6
32445cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 7706
  • sample type: soil
  • geographic location: Okinawa main island, Yambaru area, Ryukyu Archipelago
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

  • @ref: 7706
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Shinella yambaruensis gene for 16S rRNA, partial sequence, strain: NBRC 102122AB6817071411nuccore415996
7706Shinella yambaruensis gene for 16S rRNA, partial sequence, strain: MS4AB2854811443nuccore415996

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shinella yambaruensis DSM 18801GCA_022899355scaffoldncbi415996
66792Shinella yambaruensis DSM 18801GCA_025656855scaffoldncbi415996

GC content

  • @ref: 7706
  • GC-content: 66.4

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno98.5yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.326yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes85.278yes
69480spore-formingspore-formingAbility to form endo- or exosporesno93.236yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.75yes
69480flagellatedmotile2+Ability to perform flagellated movementyes68.309no

External links

@ref: 7706

culture collection no.: DSM 18801, NBRC 102122

straininfo link

  • @ref: 83080
  • straininfo: 397399

literature

  • topic: Phylogeny
  • Pubmed-ID: 19244436
  • title: Shinella yambaruensis sp. nov., a 3-methyl-sulfolane-assimilating bacterium isolated from soil.
  • authors: Matsui T, Shinzato N, Tamaki H, Muramatsu M, Hanada S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65510-0
  • year: 2009
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Mesylates/*metabolism, Molecular Sequence Data, Nitrates/metabolism, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/genetics/isolation & purification/physiology, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7706Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18801)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18801
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
32445Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128667
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
83080Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397399.1StrainInfo: A central database for resolving microbial strain identifiers