Strain identifier

BacDive ID: 23071

Type strain: Yes

Species: Pedococcus badiiscoriae

Strain Designation: Sco-B23

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 642776 (species)

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General

@ref: 19266

BacDive-ID: 23071

DSM-Number: 23987

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped

description: Pedococcus badiiscoriae Sco-B23 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from volcanic ash .

NCBI tax id

  • NCBI tax id: 642776
  • Matching level: species

strain history

@refhistory
19266<- S. D. Lee, Jeju National Univ., Rep. of Korea; Sco-B23
67771<- SD Lee, Cheju Univ.

doi: 10.13145/bacdive23071.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Pedococcus
  • species: Pedococcus badiiscoriae
  • full scientific name: Pedococcus badiiscoriae (Lee 2013) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Phycicoccus badiiscoriae

@ref: 19266

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Pedococcus

species: Pedococcus badiiscoriae

full scientific name: Pedococcus badiiscoriae (Lee 2013) Nouioui et al. 2018

strain designation: Sco-B23

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30673positive0.2 µm0.2 µmcoccus-shapedno
67771coccus-shapedno
67771positive
69480no96.057
69480positive100

pigmentation

  • @ref: 30673
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 19266
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
19266positivegrowth28mesophilic
30673positivegrowth20-35
30673positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30673positivegrowth5.1-11.1alkaliphile
30673positiveoptimum8.6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30673aerobe
67771aerobe

spore formation

@refspore formationconfidence
30673no
69481no98
69480no99.992

halophily

  • @ref: 30673
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

observation

  • @ref: 67771
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3067317234glucose+carbon source
3067325115malate+carbon source
3067317306maltose+carbon source
3067337684mannose+carbon source
30673506227N-acetylglucosamine+carbon source
306734853esculin+hydrolysis

enzymes

@refvalueactivityec
30673acid phosphatase+3.1.3.2
30673alkaline phosphatase+3.1.3.1
30673catalase+1.11.1.6
30673gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19266volcanic ash (scoria)Jeju, near the small mountain Darangshi OreumRepublic of KoreaKORAsia
67771From volcanic ash (scoria)JejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Dust
#Environmental#Terrestrial#Volcanic

taxonmaps

  • @ref: 69479
  • File name: preview.99_4206.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_670;97_776;98_900;99_4206&stattab=map
  • Last taxonomy: Pedococcus
  • 16S sequence: FN386744
  • Sequence Identity:
  • Total samples: 5554
  • soil counts: 3476
  • aquatic counts: 473
  • animal counts: 999
  • plant counts: 606

Safety information

risk assessment

  • @ref: 19266
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19266
  • description: Phycicoccus badiiscoriae partial 16S rRNA gene, type strain Sco-B23T
  • accession: FN386744
  • length: 1433
  • database: ena
  • NCBI tax ID: 642776

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedococcus badiiscoriae DSM 23987GCA_013408925contigncbi642776
66792Phycicoccus badiiscoriae strain DSM 23987642776.3wgspatric642776
66792Phycicoccus badiiscoriae DSM 239872844619028draftimg642776

GC content

@refGC-contentmethod
1926669.7high performance liquid chromatography (HPLC)
3067369.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
gram-positiveyes90.015yes
anaerobicno97.743no
halophileno97.195no
spore-formingno92.605yes
glucose-utilyes86.189no
thermophileno88.675yes
flagellatedno98.67no
aerobicyes91.13yes
motileno97.521yes
glucose-fermentno90.605no

External links

@ref: 19266

culture collection no.: DSM 23987, KACC 15111, KCTC 19807, NBRC 107918

straininfo link

  • @ref: 87309
  • straininfo: 399376

literature

  • topic: Phylogeny
  • Pubmed-ID: 22685104
  • title: Phycicoccus badiiscoriae sp. nov., a novel actinomycete isolated from scoria.
  • authors: Lee SD
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.041699-0
  • year: 2012
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19266Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23987)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23987
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
30673Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2700428776041
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
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
87309Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399376.1StrainInfo: A central database for resolving microbial strain identifiers