Strain identifier

BacDive ID: 7663

Type strain: Yes

Species: Kocuria turfanensis

Strain Designation: HO-9042

Strain history: <- X Luo, CCTCC, China

NCBI tax ID(s): 388357 (species)

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General

@ref: 16162

BacDive-ID: 7663

DSM-Number: 22143

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

description: Kocuria turfanensis HO-9042 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from air.

NCBI tax id

  • NCBI tax id: 388357
  • Matching level: species

strain history

@refhistory
16162<- C.-X. Fang, CCTCC; CCTCC AB 206107
67770KCTC 19307 <-- C. Fang HO-9042.
67771<- X Luo, CCTCC, China

doi: 10.13145/bacdive7663.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Kocuria
  • species: Kocuria turfanensis
  • full scientific name: Kocuria turfanensis Zhou et al. 2008

@ref: 16162

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Kocuria

species: Kocuria turfanensis

full scientific name: Kocuria turfanensis Zhou et al. 2008 emend. Camacho et al. 2017 emend. Nouioui et al. 2018

strain designation: HO-9042

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32328positivecoccus-shapedno
67771positive
69480no95.174
69480positive100

Culture and growth conditions

culture medium

  • @ref: 16162
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
16162positivegrowth28mesophilic
32328positivegrowth30-40
67770positivegrowth35mesophilic
67771positivegrowth35mesophilic

culture pH

  • @ref: 32328
  • ability: positive
  • type: growth
  • pH: 6.5-9
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32328aerobe
67771aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.995

halophily

  • @ref: 32328
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-15 %

observation

@refobservation
67770quinones: MK-8(H2), MK-9(H2), MK-7(H2)
67771quinones: MK-8(H2), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3232840585alpha-cyclodextrin+carbon source
3232828260galactose+carbon source
3232817596inosine+carbon source
3232829864mannitol+carbon source
3232828053melibiose+carbon source
3232817268myo-inositol+carbon source
3232851850methyl pyruvate+carbon source
3232816634raffinose+carbon source
3232827082trehalose+carbon source
3232817632nitrate+reduction

enzymes

  • @ref: 32328
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16162airXinjiangChinaCHNAsia
67770AirXinjiangChinaCHNAsia
67771From airXinjiangChinaCHNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Air

taxonmaps

  • @ref: 69479
  • File name: preview.99_4042.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_424;97_1751;98_2142;99_4042&stattab=map
  • Last taxonomy: Kocuria
  • 16S sequence: DQ531634
  • Sequence Identity:
  • Total samples: 378
  • soil counts: 69
  • aquatic counts: 42
  • animal counts: 266
  • plant counts: 1

Safety information

risk assessment

  • @ref: 16162
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16162
  • description: Kocuria turfanensis strain HO-9042 16S ribosomal RNA gene, partial sequence
  • accession: DQ531634
  • length: 1441
  • database: ena
  • NCBI tax ID: 388357

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kocuria turfanensis HO-9042GCA_001580365chromosomencbi388357
66792Kocuria turfanensis NBRC 107627GCA_007992155contigncbi388357
66792Kocuria turfanensis strain NBRC 107627388357.9wgspatric388357
66792Kocuria turfanensis HO-90422687453620completeimg388357

GC content

@refGC-contentmethod
1616265.0high performance liquid chromatography (HPLC)
3232865
6777072.8genome sequence analysis
6777065high performance liquid chromatography (HPLC)
6777165.0

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 79
  • training_data: no

External links

@ref: 16162

culture collection no.: DSM 22143, CCTCC AB 206107, KCTC 19307, JCM 15622, NBRC 107627

straininfo link

  • @ref: 77107
  • straininfo: 402036

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18523169Kocuria flava sp. nov. and Kocuria turfanensis sp. nov., airborne actinobacteria isolated from Xinjiang, China.Zhou G, Luo X, Tang Y, Zhang L, Yang Q, Qiu Y, Fang CInt J Syst Evol Microbiol10.1099/ijs.0.65323-02008*Air Microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Micrococcaceae/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny26048314Kocuria dechangensis sp. nov., an actinobacterium isolated from saline and alkaline soils.Wang K, Zhang L, Liu Y, Pan Y, Meng L, Xu T, Zhang C, Liu H, Hong S, Huang H, Jiang JInt J Syst Evol Microbiol10.1099/ijs.0.0003722015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Micrococcaceae/classification, Molecular Sequence Data, Nucleic Acid Hybridization/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/analysis, Soil/chemistry, Soil MicrobiologyGenetics
Genetics26971972Genome sequencing and annotation of Kocuria turfanensis HO-9042, to promote explorating high-salt resistance associated gene resources.Dai J, Yu C, Huang Z, Fan M, Jia Z, Li X, Wang Z, Li Z, Yao J, Li P, Zheng G, Chen XJ Biotechnol10.1016/j.jbiotec.2016.03.0132016Base Composition, Genome Size, *Genome, Bacterial, Micrococcaceae/*genetics, Molecular Sequence Annotation, Sequence Analysis, DNA/*methodsTranscriptome
Phylogeny27902231Kocuria oceani sp. nov., isolated from a deep-sea hydrothermal plume.Zhang L, Xi L, Ruan J, Huang YInt J Syst Evol Microbiol10.1099/ijsem.0.0015992017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrothermal Vents/*microbiology, Micrococcaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome
Phylogeny29034846Kocuria salina sp. nov., an actinobacterium isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum and emended description of Kocuria turfanensis.Camacho M, Redondo-Gomez S, Rodriguez-Llorente I, Rohde M, Sproer C, Schumann P, Klenk HP, Montero-Calasanz MDCInt J Syst Evol Microbiol10.1099/ijsem.0.0024012017Amaranthaceae/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Micrococcaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Salt-Tolerant Plants/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Spain, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16162Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22143)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22143
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
32328Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2856228776041
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
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)
77107Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402036.1StrainInfo: A central database for resolving microbial strain identifiers