Strain identifier

BacDive ID: 14867

Type strain: Yes

Species: Kitasatospora viridis

Strain Designation: 52108a

Strain history: CGMCC 4.1878 <-- Z. Liu 52108a.

NCBI tax ID(s): 281105 (species)

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General

@ref: 12008

BacDive-ID: 14867

DSM-Number: 44826

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive

description: Kitasatospora viridis 52108a is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil rhizosphere of wild tea plant .

NCBI tax id

  • NCBI tax id: 281105
  • Matching level: species

strain history

@refhistory
12008<- Y. Zhou; AS 4.1878
67770CGMCC 4.1878 <-- Z. Liu 52108a.

doi: 10.13145/bacdive14867.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kitasatosporales
  • family: Streptomycetaceae
  • genus: Kitasatospora
  • species: Kitasatospora viridis
  • full scientific name: Kitasatospora viridis Liu et al. 2005

@ref: 12008

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Kitasatospora

species: Kitasatospora viridis

full scientific name: Kitasatospora viridis Liu et al. 2005

strain designation: 52108a

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
31330positiveno
69480positive100

pigmentation

  • @ref: 31330
  • production: no

multimedia

  • @ref: 12008
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44826.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12008ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
12008GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
12008STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://mediadive.dsmz.de/medium/252Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
12008positivegrowth28mesophilic
31330positivegrowth10-37
31330positiveoptimum23.5psychrophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31330positivegrowth04-07acidophile
31330positiveoptimum5.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31330
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31330yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
31330NaClpositivegrowth<10 %
31330NaClpositiveoptimum5 %

observation

@refobservation
31330aggregates in chains
67770quinones: MK-9(H6), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3133015963ribitol+carbon source
3133016449alanine+carbon source
3133029016arginine+carbon source
3133017057cellobiose+carbon source
3133028757fructose+carbon source
3133028260galactose+carbon source
3133024265gluconate+carbon source
3133017234glucose+carbon source
3133029987glutamate+carbon source
3133027570histidine+carbon source
3133017716lactose+carbon source
3133017306maltose+carbon source
3133029864mannitol+carbon source
3133037684mannose+carbon source
3133028053melibiose+carbon source
3133028044phenylalanine+carbon source
3133016634raffinose+carbon source
3133026546rhamnose+carbon source
3133017814salicin+carbon source
3133030911sorbitol+carbon source
3133017992sucrose+carbon source
3133026986threonine+carbon source
3133027082trehalose+carbon source
3133017151xylitol+carbon source

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
12008soil rhizosphere of wild tea plant (Camellia oleifera)Camellia oleiferaJiangxiChinaCHNAsia
67770Rhizosphere soil of wild tea plants (Camellia oleifera) growing on Jiangxi Agric. Univ.Camellia oleiferaJiangxi ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

  • @ref: 12008
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 31330
  • description: Kitasatospora viridis 16S ribosomal RNA gene, partial sequence
  • accession: AY613990
  • length: 1422
  • database: nuccore
  • NCBI tax ID: 281105

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kitasatospora viridis DSM 44826GCA_007829815contigncbi281105
66792Kitasatospora viridis strain DSM 44826281105.3wgspatric281105
66792Kitasatospora viridis DSM 448262818991472draftimg281105

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.266yes
gram-positiveyes91.715yes
anaerobicno99.366yes
halophileno88.883yes
spore-formingyes93.988yes
glucose-utilyes91.751yes
flagellatedno98.484yes
aerobicyes93.121no
thermophileno97.944yes
glucose-fermentno88.674no

External links

@ref: 12008

culture collection no.: DSM 44826, AS 4.1878, JCM 14111, CGMCC 4.1878

straininfo link

  • @ref: 83980
  • straininfo: 138010

literature

  • topic: Phylogeny
  • Pubmed-ID: 15774648
  • title: Kitasatospora viridis sp. nov., a novel actinomycete from soil.
  • authors: Liu Z, Rodriguez C, Wang L, Cui Q, Huang Y, Quintana ET, Goodfellow M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63329-0
  • year: 2005
  • mesh: Camellia/*microbiology, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomycetaceae/*classification/genetics/isolation & purification/physiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
12008Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44826)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44826
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
31330Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2764428776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83980Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138010.1StrainInfo: A central database for resolving microbial strain identifiers