Strain identifier

BacDive ID: 6319

Type strain: Yes

Species: Kineococcus xinjiangensis

Strain Designation: S2-20

Strain history: CIP <- 2010, CCTCC <- M. Liu, Wuhan Univ., Wuhan, China: strain S2-20

NCBI tax ID(s): 512762 (species)

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

@ref: 16492

BacDive-ID: 6319

DSM-Number: 22857

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

description: Kineococcus xinjiangensis S2-20 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from desert sand.

NCBI tax id

  • NCBI tax id: 512762
  • Matching level: species

strain history

@refhistory
16492<- KCTC; KCTC 19474
67770KCTC 19474 <-- CCTCC AB 207179 <-- M. Liu and F. Peng S2-20.
67771<- M Liu, CCTCC, China
123983CIP <- 2010, CCTCC <- M. Liu, Wuhan Univ., Wuhan, China: strain S2-20

doi: 10.13145/bacdive6319.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kineosporiales
  • family: Kineosporiaceae
  • genus: Kineococcus
  • species: Kineococcus xinjiangensis
  • full scientific name: Kineococcus xinjiangensis Liu et al. 2009

@ref: 16492

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kineosporiaceae

genus: Kineococcus

species: Kineococcus xinjiangensis

full scientific name: Kineococcus xinjiangensis Liu et al. 2009 emend. Nouioui et al. 2018

strain designation: S2-20

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29018positivecoccus-shapedyes
67771positive
69480positive100
123983positiveoval-shapedyes

colony morphology

@refcolony colorincubation periodmedium used
19800Maize yellow10-14 daysISP 2
19800Golden yellow10-14 daysISP 3
19800Grey white10-14 daysISP 4
19800Grey white10-14 daysISP 5
19800Sulfur yellow10-14 daysISP 6
19800Cream10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19800noISP 2
19800noISP 3
19800noISP 4
19800noISP 5
19800noISP 6
19800noISP 7

pigmentation

  • @ref: 29018
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16492R2A 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
19800ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19800ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19800ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19800ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19800ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19800ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
37919MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123983CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123983CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
16492positivegrowth28mesophilic
19800positiveoptimum28mesophilic
29018positivegrowth14-40
29018positiveoptimum37mesophilic
37919positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
29018positivegrowth06-10alkaliphile
29018positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29018aerobe
67771aerobe
123983obligate aerobe

spore formation

@refspore formationconfidence
29018no
69481no98
69480no96.607

halophily

@refsaltgrowthtested relationconcentration
29018NaClpositivegrowth<2 %
29018NaClpositiveoptimum0.5 %

observation

@refobservation
29018aggregates in clumps
67770quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1980062968cellulose+
1980016634raffinose+
1980026546rhamnose+
1980028757fructose+
1980029864mannitol+
1980017268myo-inositol+
1980018222xylose+
1980017992sucrose+
1980022599arabinose+
1980017234glucose+
2901822599arabinose+carbon source
2901828260galactose+carbon source
2901817234glucose+carbon source
2901817306maltose+carbon source
2901826546rhamnose+carbon source
2901817992sucrose+carbon source
290184853esculin+hydrolysis
12398317632nitrate-reduction
12398316301nitrite-reduction
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 123983
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29018catalase+1.11.1.6
29018gelatinase+
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
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase+3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
123983oxidase-
123983catalase+1.11.1.6
123983urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19800+-+++++++-++-+/--+++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19800+++-+----++++++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
16492desert sandXinjiang ProvinceChinaCHNAsia
67770Desert sandXinjiang ProvinceChinaCHNAsia
67771From desert sandXinjiang ProvinceChinaCHNAsia
123983Environment, Sand sampleXinjiang desertChinaCHNAsia2007

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Sandy
#Condition#Xerophilic

taxonmaps

  • @ref: 69479
  • File name: preview.99_141660.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_13736;97_16722;98_20758;99_141660&stattab=map
  • Last taxonomy: Kineococcus xinjiangensis
  • 16S sequence: EU543662
  • Sequence Identity:
  • Total samples: 53
  • soil counts: 32
  • aquatic counts: 6
  • animal counts: 8
  • plant counts: 7

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
164921Risk group (German classification)
1239831Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16492
  • description: Kineococcus xinjiangensis strain S2-20 16S ribosomal RNA gene, partial sequence
  • accession: EU543662
  • length: 1385
  • database: ena
  • NCBI tax ID: 512762

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kineococcus xinjiangensis strain DSM 22857512762.3wgspatric512762
66792Kineococcus xinjiangensis DSM 228572731639219draftimg512762
67770Kineococcus xinjiangensis DSM 22857GCA_002934625contigncbi512762

GC content

@refGC-contentmethod
1649277.8
6777077.8high performance liquid chromatography (HPLC)
6777074.6genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
gram-positiveyes93.887yes
anaerobicno99.343no
halophileno80.546no
spore-formingno71.188no
glucose-utilyes86.895yes
aerobicyes92.711yes
thermophileno98.148no
motileyes79.47yes
flagellatedno86.887no
glucose-fermentno71.445yes

External links

@ref: 16492

culture collection no.: DSM 22857, KCTC 19474, CCTCC AB 207179, JCM 16219, NBRC 107624, CIP 110123

straininfo link

  • @ref: 75793
  • straininfo: 362801

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19406798Kineococcus xinjiangensis sp. nov., isolated from desert sand.Liu M, Peng F, Wang Y, Zhang K, Chen G, Fang CInt J Syst Evol Microbiol10.1099/ijs.0.004168-02009Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, *Desert Climate, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, *Soil Microbiology, Species SpecificityGenetics
Phylogeny22467136Kineococcus glutineturens sp. nov., isolated from soil in Yunnan, south-west China.Nie GX, Ming H, Zhang J, Feng HG, Li S, Yu TT, Zhou EM, Tang SK, Li WJAntonie Van Leeuwenhoek10.1007/s10482-012-9731-12012Actinomycetales/*classification/genetics/*isolation & purification, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny27502175Thalassiella azotovora gen. nov., sp. nov., a New Member of the Family Kineosporiaceae Isolated from Sea Water in South Korea.Lee D, Jang JH, Cha S, Seo TCurr Microbiol10.1007/s00284-016-1112-y2016Actinomycetales/classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiologyMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16492Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22857)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22857
19800Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM22857.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
29018Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2544828776041
37919Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7946
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
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
75793Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362801.1StrainInfo: A central database for resolving microbial strain identifiers
123983Curators of the CIPCollection of Institut Pasteur (CIP 110123)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110123