Strain identifier

BacDive ID: 7496

Type strain: Yes

Species: Microcella alkalica

Strain Designation: KSL-113

Strain history: CIP <- 2005, J.H. Yoon, KRIBB, Taejon, Korea: strain KSL-113

NCBI tax ID(s): 355930 (species)

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General

@ref: 8240

BacDive-ID: 7496

DSM-Number: 19663

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

description: Microcella alkalica KSL-113 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from alkaline soil.

NCBI tax id

  • NCBI tax id: 355930
  • Matching level: species

strain history

@refhistory
8240<- CIP <- J.-H. Yoon, strain KSL-113
67770CIP 108920 <-- J.-H. Yoon KSL-113.
67771<- JH Yoon, KRIBB
116243CIP <- 2005, J.H. Yoon, KRIBB, Taejon, Korea: strain KSL-113

doi: 10.13145/bacdive7496.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microcella
  • species: Microcella alkalica
  • full scientific name: Microcella alkalica Xie et al. 2022

  • synonyms

    • @ref: 20215
    • synonym: Yonghaparkia alkaliphila

@ref: 8240

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micrococcales

family: Microbacteriaceae

genus: Microcella

species: Microcella alkalica

full scientific name: Microcella alkalica (Yoon et al. 2006), Xie et al. 2022

strain designation: KSL-113

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
67771positive
69480positive100
116243positiverod-shapedno

colony morphology

  • @ref: 116243
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8240TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
38366MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
116243CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
8240positivegrowth28mesophilic
38366positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
116243positivegrowth15-30
116243nogrowth5psychrophilic
116243nogrowth10psychrophilic
116243nogrowth37mesophilic
116243nogrowth41thermophilic
116243nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
116243obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
116243NaClnogrowth0 %
116243NaClnogrowth2 %
116243NaClnogrowth4 %
116243NaClnogrowth6 %
116243NaClnogrowth8 %
116243NaClnogrowth10 %

murein

  • @ref: 8240
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

  • @ref: 67770
  • observation: quinones: MK-12, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11624316947citrate-carbon source
1162434853esculin+hydrolysis
116243606565hippurate+hydrolysis
11624317632nitrate-reduction
11624316301nitrite-reduction
11624315792malonate-assimilation
11624317632nitrate-respiration

metabolite production

  • @ref: 116243
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11624315688acetoin-
11624317234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
116243oxidase-
116243beta-galactosidase+3.2.1.23
116243alcohol dehydrogenase-1.1.1.1
116243gelatinase-
116243amylase+
116243DNase-
116243caseinase-3.4.21.50
116243catalase+1.11.1.6
116243tween esterase-
116243gamma-glutamyltransferase+2.3.2.2
116243lecithinase-
116243lipase-
116243lysine decarboxylase-4.1.1.18
116243ornithine decarboxylase-4.1.1.17
116243phenylalanine ammonia-lyase-4.3.1.24
116243protease-
116243tryptophan deaminase-
116243urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116243--++-+-----+---+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
8240alkaline soilRepublic of KoreaKORAsia
67770Alkaline soilRepublic of KoreaKORAsiaKwangchun
67771From soilRepublic of KoreaKORAsia
116243Environment, Alkaline soilRepublic of KoreaKORAsiaKwangchun2003

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Alkaline

taxonmaps

  • @ref: 69479
  • File name: preview.99_6039.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2880;97_3539;98_4480;99_6039&stattab=map
  • Last taxonomy: Yonghaparkia alkaliphila subclade
  • 16S sequence: DQ256087
  • Sequence Identity:
  • Total samples: 2008
  • soil counts: 660
  • aquatic counts: 607
  • animal counts: 338
  • plant counts: 403

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82401Risk group (German classification)
1162431Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8240
  • description: Yonghaparkia alkaliphila strain KSL-113 16S ribosomal RNA gene, partial sequence
  • accession: DQ256087
  • length: 1476
  • database: ena
  • NCBI tax ID: 355930

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microcella alkalica DSM 19663GCA_014137945contigncbi355930
66792Yonghaparkia alkaliphila strain DSM 19663355930.3wgspatric355930
66792Yonghaparkia alkaliphila DSM 196632820983214draftimg355930

GC content

@refGC-contentmethod
824071
6777071.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes94.147no
anaerobicno98.511yes
halophileno91.774no
spore-formingno90.984no
glucose-utilyes83.077no
motileno91.699no
flagellatedno97.69no
aerobicyes94.082no
thermophileno98.307yes
glucose-fermentno90.52no

External links

@ref: 8240

culture collection no.: DSM 19663, CIP 108920, KCTC 19126, JCM 15138, NBRC 106160

straininfo link

  • @ref: 76942
  • straininfo: 297347

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17012572Yonghaparkia alkaliphila gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an alkaline soil.Yoon JH, Kang SJ, Schumann P, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64258-02006Actinomycetales/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal, Fatty Acids/analysis, Genes, rRNA, Genotype, Hydrogen-Ion Concentration, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny34628559Microcella flavibacter sp. nov., isolated from marine sediment, and reclassification of Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila as Microcella frigidaquae comb. nov., Microcella indica nom. nov., and Microcella alkalica nom. nov.Xie F, Pei S, Huang X, Wang L, Kou J, Zhang GAntonie Van Leeuwenhoek10.1007/s10482-021-01668-72021Actinobacteria, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Fatty Acids/analysis, *Geologic Sediments, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2Transcriptome

Reference

@idauthorscataloguedoi/urltitle
8240Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19663)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19663
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
38366Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6603
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
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
76942Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297347.1StrainInfo: A central database for resolving microbial strain identifiers
116243Curators of the CIPCollection of Institut Pasteur (CIP 108920)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108920