Strain identifier

BacDive ID: 134117

Type strain: Yes

Species: Paracoccus koreensis

Strain Designation: Ch05

Strain history: CIP <- 2005, IAM <- ST Lee, KAIST: strain Ch05

NCBI tax ID(s): 290306 (species)

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General

@ref: 31414

BacDive-ID: 134117

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

description: Paracoccus koreensis Ch05 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from Granules used in the wastewater-treatment plant of a beer-brewing factory in Chung-Won.

NCBI tax id

  • NCBI tax id: 290306
  • Matching level: species

strain history

@refhistory
383452005, IAM
67770IAM 15216 <-- S.-T. Lee Ch05.
67771<- ST Lee, KAIST
120481CIP <- 2005, IAM <- ST Lee, KAIST: strain Ch05

doi: 10.13145/bacdive134117.20230509.8.1

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 koreensis
  • full scientific name: Paracoccus koreensis La et al. 2005

@ref: 31414

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus koreensis

strain designation: Ch05

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31414negative1.25 µm0.75 µmrod-shapedno
67771negative
120481negativerod-shapedno

pigmentation

  • @ref: 31414
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
38345MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
120481CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
31414positivegrowth15-37
31414positiveoptimum26mesophilic
38345positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic
120481positivegrowth25-41
120481nogrowth5psychrophilic
120481nogrowth10psychrophilic

culture pH

@refabilitytypepH
31414positivegrowth06-08
31414positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31414aerobe
67771aerobe
120481obligate aerobe

spore formation

  • @ref: 31414
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
120481NaClpositivegrowth0-4 %
120481NaClnogrowth6 %
120481NaClnogrowth8 %
120481NaClnogrowth10 %

observation

@refobservation
31414aggregates in clumps
67770quinones: Q-10
67771quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3141416449alanine+carbon source
3141428087glycogen+carbon source
3141427570histidine+carbon source
3141426271proline+carbon source
3141433942ribose+carbon source
3141430911sorbitol+carbon source
3141431011valerate+carbon source
1204814853esculin-hydrolysis
12048117632nitrate+reduction
12048116301nitrite+reduction
12048117632nitrate-respiration

metabolite production

  • @ref: 120481
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 120481
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
31414catalase+1.11.1.6
31414cytochrome oxidase+1.9.3.1
120481oxidase+
120481beta-galactosidase+3.2.1.23
120481alcohol dehydrogenase-1.1.1.1
120481gelatinase-
120481amylase-
120481DNase-
120481caseinase-3.4.21.50
120481catalase+1.11.1.6
120481tween esterase-
120481lecithinase-
120481lipase-
120481lysine decarboxylase-4.1.1.18
120481ornithine decarboxylase-4.1.1.17
120481protease-
120481tryptophan deaminase+
120481urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120481-+++-+---+----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
67770Granules used in the wastewater-treatment plant of a beer-brewing factory in Chung-WonRepublic of KoreaKORAsia
67771From granule sludgeRepublic of KoreaKORAsiaChungjoo
120481Environment, Granules in the treatment of wastewater from a beer-brewing factoryRepublic of KoreaKORAsiaChungjoo

taxonmaps

  • @ref: 69479
  • File name: preview.99_177589.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_4950;97_44361;98_58012;99_177589&stattab=map
  • Last taxonomy: Paracoccus koreensis subclade
  • 16S sequence: AB187584
  • Sequence Identity:
  • Total samples: 110
  • soil counts: 54
  • aquatic counts: 31
  • animal counts: 21
  • plant counts: 4

Safety information

risk assessment

  • @ref: 120481
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31414
  • description: Paracoccus koreensis gene for 16S rRNA, partial sequence, strain:Ch05
  • accession: AB187584
  • length: 1386
  • database: nuccore
  • NCBI tax ID: 290306

GC content

@refGC-contentmethod
3141469
6777169.0
6777069high performance liquid chromatography (HPLC)

External links

@ref: 31414

culture collection no.: KCTC 12238, IAM 15216, JCM 21670, NBRC 102292, CIP 108862

straininfo link

  • @ref: 91719
  • straininfo: 132665

literature

  • topic: Phylogeny
  • Pubmed-ID: 16014497
  • title: Paracoccus koreensis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket (UASB) reactor.
  • authors: La HJ, Im WT, Ten LN, Kang MS, Shin DY, Lee ST
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63494-0
  • year: 2005
  • mesh: Anaerobiosis, Bacterial Typing Techniques, *Bioreactors, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/*growth & development/isolation & purification, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
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
31414Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172772128776041
38345Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6539
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91719Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID132665.1
120481Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108862Collection of Institut Pasteur (CIP 108862)