Strain identifier

BacDive ID: 133854

Type strain: Yes

Species: Paracoccus tibetensis

Strain Designation: Tibet-S9a3

NCBI tax ID(s): 336292 (species)

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General

@ref: 30682

BacDive-ID: 133854

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped

description: Paracoccus tibetensis Tibet-S9a3 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 336292
  • Matching level: species

doi: 10.13145/bacdive133854.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Paracoccus
  • species: Paracoccus tibetensis
  • full scientific name: Paracoccus tibetensis Zhu et al. 2013

@ref: 30682

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus tibetensis

strain designation: Tibet-S9a3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30682negative1 µm0.7 µmrod-shapedno
69480negative99.982

pigmentation

  • @ref: 30682
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30682positivegrowth10-35
30682positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
30682positivegrowth8.5-13alkaliphile
30682positiveoptimum9.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30682
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30682no
69481no100
69480no99.999

halophily

  • @ref: 30682
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3068230089acetate+carbon source
3068221217L-alaninamide+carbon source
3068216449alanine+carbon source
3068240585alpha-cyclodextrin+carbon source
30682286442-oxopentanoate+carbon source
3068222599arabinose+carbon source
3068222653asparagine+carbon source
3068235391aspartate+carbon source
3068216947citrate+carbon source
3068215740formate+carbon source
3068228757fructose+carbon source
3068233984fucose+carbon source
3068224175galacturonate+carbon source
306825417glucosamine+carbon source
3068217234glucose+carbon source
3068232323glucuronamide+carbon source
3068229987glutamate+carbon source
3068217754glycerol+carbon source
3068228087glycogen+carbon source
3068217596inosine+carbon source
3068224996lactate+carbon source
3068225115malate+carbon source
3068217306maltose+carbon source
3068229864mannitol+carbon source
3068226271proline+carbon source
3068217272propionate+carbon source
3068251850methyl pyruvate+carbon source
3068216634raffinose+carbon source
3068217822serine+carbon source
3068230911sorbitol+carbon source
3068230031succinate+carbon source
3068217992sucrose+carbon source
3068226986threonine+carbon source
3068227082trehalose+carbon source
3068216704uridine+carbon source
3068217151xylitol+carbon source
306824853esculin+hydrolysis

enzymes

@refvalueactivityec
30682acid phosphatase+3.1.3.2
30682alkaline phosphatase+3.1.3.1
30682catalase+1.11.1.6
30682gelatinase+

Isolation, sampling and environmental information

isolation

  • @ref: 30682
  • sample type: soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Sequence information

16S sequences

  • @ref: 30682
  • description: Paracoccus tibetensis strain Tibet-S9a3 16S ribosomal RNA gene, partial sequence
  • accession: DQ108402
  • length: 1449
  • database: nuccore
  • NCBI tax ID: 336292

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus tibetensis CGMCC 1.8925GCA_900102505scaffoldncbi336292
66792Paracoccus tibetensis strain CGMCC 1.8925336292.4wgspatric336292
66792Paracoccus tibetense CGMCC 1.89252596583549draftimg336292

GC content

  • @ref: 30682
  • GC-content: 69.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno83.484no
gram-positiveno97.811yes
anaerobicno97.376no
aerobicyes92.584yes
halophileno64.376no
spore-formingno95.393no
glucose-fermentno86.78no
thermophileno96.796yes
glucose-utilyes93.325yes
motileno58.591no

External links

@ref: 30682

culture collection no.: CGMCC 1.8925, NBRC 105667

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23024140Paracoccus tibetensis sp. nov., isolated from Qinghai-Tibet Plateau permafrost.Zhu S, Zhao Q, Zhang G, Jiang Z, Sheng H, Feng H, An LInt J Syst Evol Microbiol10.1099/ijs.0.041905-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analysisGenetics
Phylogeny28598318Paracoccus hibisci sp. nov., isolated from the rhizosphere of Hibiscus syriacus L. (Mugunghwa flower).Yan ZF, Moya G, Lin P, Won KH, Yang JE, Li CT, Kook M, Wang QJ, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0018742017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hibiscus/*microbiology, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny29484518Paracoccus pueri sp. nov., isolated from Pu'er tea.Wang YS, Yan ZF, Lin P, Gao W, Yi THAntonie Van Leeuwenhoek10.1007/s10482-018-1041-92018Base Composition, Carbohydrate Metabolism, China, Fatty Acids/chemistry, Flagella, Nucleic Acid Hybridization, Paracoccus/chemistry/*classification/genetics, Phenotype, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Tea/*microbiology, Ubiquinone/chemistryPhenotype

Reference

@idauthorstitledoi/urlID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
30682Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172701328776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1