Strain identifier

BacDive ID: 133454

Type strain: Yes

Species: Paracoccus chinensis

Strain Designation: KS-11

NCBI tax ID(s): 525640 (species)

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

@ref: 29041

BacDive-ID: 133454

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

description: Paracoccus chinensis KS-11 is an aerobe, Gram-negative, motile bacterium that was isolated from freshwater sediment .

NCBI tax id

  • NCBI tax id: 525640
  • Matching level: species

doi: 10.13145/bacdive133454.20230509.8.1

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 chinensis
  • full scientific name: Paracoccus chinensis Li et al. 2009

@ref: 29041

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus chinensis

strain designation: KS-11

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29041negative1.75 µm1.15 µmovoid-shapedyes
69480negative99.99

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
29041positivegrowth25-40
29041positiveoptimum28-37mesophilic

culture pH

@refabilitytypepHPH range
29041positivegrowth6-9.5alkaliphile
29041positiveoptimum7.5-9

Physiology and metabolism

oxygen tolerance

  • @ref: 29041
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29041no
69481no100
69480no99.993

halophily

  • @ref: 29041
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

observation

  • @ref: 29041
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2904130089acetate+carbon source
2904116449alanine+carbon source
2904122653asparagine+carbon source
2904116947citrate+carbon source
2904128757fructose+carbon source
2904133984fucose+carbon source
2904128260galactose+carbon source
2904124265gluconate+carbon source
2904117234glucose+carbon source
2904127570histidine+carbon source
2904117716lactose+carbon source
2904117306maltose+carbon source
2904137684mannose+carbon source
2904128053melibiose+carbon source
2904126271proline+carbon source
2904115361pyruvate+carbon source
2904133942ribose+carbon source
2904117814salicin+carbon source
2904130911sorbitol+carbon source
2904117992sucrose+carbon source
2904127082trehalose+carbon source
2904118222xylose+carbon source
2904117632nitrate+reduction

enzymes

@refvalueactivityec
29041catalase+1.11.1.6
29041cytochrome oxidase+1.9.3.1
29041urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 29041
  • sample type: freshwater sediment (river, lake, pond)

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Pond (small)
#Environmental#Aquatic#River (Creek)

taxonmaps

  • @ref: 69479
  • File name: preview.99_11251.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1674;97_3137;98_8401;99_11251&stattab=map
  • Last taxonomy: Paracoccus
  • 16S sequence: EU660389
  • Sequence Identity:
  • Total samples: 16440
  • soil counts: 1527
  • aquatic counts: 4482
  • animal counts: 9541
  • plant counts: 890

Sequence information

16S sequences

  • @ref: 29041
  • description: Paracoccus chinensis strain KS-11 16S ribosomal RNA gene, partial sequence
  • accession: EU660389
  • length: 1362
  • database: nuccore
  • NCBI tax ID: 525640

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus chinensis CGMCC 1.7655GCA_900102885contigncbi525640
66792Paracoccus chinensis strain CGMCC 1.7655525640.3wgspatric525640
66792Paracoccus chinensis CGMCC 1.76552617270907draftimg525640

GC content

  • @ref: 29041
  • GC-content: 69

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.568yes
anaerobicno97.368yes
halophileno86.731yes
spore-formingno96.27yes
glucose-utilyes85.293yes
thermophileno93.621no
motileno59.274yes
aerobicyes88.745yes
flagellatedno91.724no
glucose-fermentno91.856no

External links

@ref: 29041

culture collection no.: CGMCC 1.7655, NBRC 104937

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19625438Paracoccus chinensis sp. nov., isolated from sediment of a reservoir.Li HF, Qu JH, Yang JS, Li ZJ, Yuan HLInt J Syst Evol Microbiol10.1099/ijs.0.004705-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Fresh Water/*microbiology, Molecular Sequence Data, Paracoccus/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny20936429Paracoccus niistensis sp. nov., isolated from forest soil, India.Dastager SG, Deepa CK, Li WJ, Tang SK, Pandey AAntonie Van Leeuwenhoek10.1007/s10482-010-9515-42010India, Paracoccus/classification/*genetics/*metabolism, Phylogeny, Polymerase Chain Reaction, Sequence Analysis, DNA, *Soil Microbiology, *TreesTranscriptome
Phylogeny30325298Paracoccus salipaludis sp. nov., isolated from saline-alkaline soil.Dong X, Zhang G, Xiong Q, Liu D, Wang D, Liu Y, Wu G, Li P, Luo Y, Zhang RInt J Syst Evol Microbiol10.1099/ijsem.0.0030652018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistryTranscriptome

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
29041Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172547128776041
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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