Strain identifier

BacDive ID: 158752

Type strain: Yes

Species: Paracoccus litorisediminis

Strain Designation: GHD-05

Strain history: <- Jung-Hoon YOON, Sungkyunkwan Univ.

NCBI tax ID(s): 2006130 (species)

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General

@ref: 65504

BacDive-ID: 158752

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

description: Paracoccus litorisediminis GHD-05 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from from tidal flat sediment.

NCBI tax id

  • NCBI tax id: 2006130
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Jung-Hoon YOON, Sungkyunkwan Univ.

doi: 10.13145/bacdive158752.20230509.8.1

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 litorisediminis
  • full scientific name: Paracoccus litorisediminis Park et al. 2017

@ref: 65504

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus litorisediminis

strain designation: GHD-05

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65504negative0.4-2.0 µm0.4-0.8 µmrod-shapedno
65504coccus-shaped
65504ovoid-shaped
69480negative99.995

colony morphology

  • @ref: 65504
  • colony size: 1.0-2.0 mm
  • colony color: yellowish white
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MA

Culture and growth conditions

culture medium

@refnamegrowthcomposition
65504Marine agar (MA)yes
65504Marine agar (MA)yessupplemented with nitrate

culture temp

@refgrowthtypetemperaturerange
65504positiveoptimum30mesophilic
65504positivegrowth10-40
65504nogrowth4psychrophilic
65504nogrowth45thermophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
65504positiveoptimum7.0-8.0
65504positivegrowth5.5
65504nogrowth5.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65504aerobe
65504anaerobe
67771aerobe

spore formation

@refspore formationconfidence
65504no
69480no99.997
69481no100

halophily

@refsaltgrowthtested relationconcentration
65504NaClpositivegrowth0-5.0 %(w/v)
65504NaClpositiveoptimum2.0 %(w/v)
65504MgCl2positivegrowth0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6550430089acetate+carbon source
6550430089acetate+energy source
6550416150benzoate-carbon source
6550416150benzoate-energy source
65504casein+hydrolysis
6550417057cellobiose+carbon source
6550417057cellobiose+energy source
6550416947citrate+carbon source
6550416947citrate+energy source
6550415824D-fructose+carbon source
6550415824D-fructose+energy source
6550412936D-galactose+carbon source
6550412936D-galactose+energy source
6550417634D-glucose+carbon source
6550417634D-glucose+energy source
6550416024D-mannose+carbon source
6550416024D-mannose+energy source
6550465327D-xylose+carbon source
6550465327D-xylose+energy source
655044853esculin-hydrolysis
6550415740formate-carbon source
6550415740formate-energy source
655045291gelatin-hydrolysis
6550417368hypoxanthine+hydrolysis
6550430849L-arabinose+carbon source
6550430849L-arabinose+energy source
6550429985L-glutamate-carbon source
6550429985L-glutamate-energy source
6550415589L-malate+carbon source
6550415589L-malate+energy source
6550417895L-tyrosine+hydrolysis
6550417306maltose-carbon source
6550417306maltose-energy source
6550417632nitrate+reduction
6550415361pyruvate+carbon source
6550415361pyruvate+energy source
6550417814salicin+carbon source
6550417814salicin+energy source
6550428017starch-hydrolysis
6550430031succinate+carbon source
6550430031succinate+energy source
6550417992sucrose-carbon source
6550417992sucrose-energy source
6550427082trehalose-carbon source
6550427082trehalose-energy source
6550453426tween 80-hydrolysis
6550415318xanthine+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6550428368novobiocinyesyes5 µg (disc)
655043542cephalothinyesyes30 µg (disc)
6550417833gentamicinyesyes30 µg (disc)
655046104kanamycinyesyes30 µg (disc)
655047507neomycinyesyes30 µg (disc)
6550427902tetracyclineyesyes30 µg (disc)
6550417076streptomycinyesyes50 µg (disc)
655043393carbenicillinyesyes100 µg (disc)
6550417698chloramphenicolyesyes100 µg (disc)
655048309polymyxin byesyes100 Unit (disc)
6550428971ampicillinyesyes10 µg (disc)
655046472lincomycinyesyes15 µg (disc)
6550416869oleandomycinyesyes15 µg (disc)
6550418208penicillin gyesyes20 Unit (disc)

metabolite production

  • @ref: 65504
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
65504catalase+1.11.1.6
65504cytochrome oxidase+1.9.3.1
65504alkaline phosphatase+3.1.3.1
65504esterase (C 4)+
65504esterase Lipase (C 8)+
65504leucine arylamidase+3.4.11.1
65504valine arylamidase+
65504cystine arylamidase+3.4.11.3
65504acid phosphatase+3.1.3.2
65504naphthol-AS-BI-phosphohydrolase+
65504alpha-glucosidase+3.2.1.20
65504N-acetyl-beta-glucosaminidase+3.2.1.52
65504lipase (C 14)-
65504trypsin-3.4.21.4
65504alpha-chymotrypsin-3.4.21.1
65504alpha-galactosidase-3.2.1.22
65504beta-galactosidase-3.2.1.23
65504beta-glucuronidase-3.2.1.31
65504beta-glucosidase-3.2.1.21
65504alpha-mannosidase-3.2.1.24
65504alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture temperatureisolation procedure
65504from tidal flat sedimentGangwha Island, Yellow SeaRepublic of KoreaKORAsiaMA25standard dilution plating technique
67771From mud flatGanghwado IslandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_65305.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_529;97_2307;98_7431;99_65305&stattab=map
  • Last taxonomy: Paracoccus
  • 16S sequence: MF193602
  • Sequence Identity:
  • Total samples: 327
  • soil counts: 43
  • aquatic counts: 92
  • animal counts: 63
  • plant counts: 129

Sequence information

16S sequences

  • @ref: 65504
  • description: 16S rRNA gene sequence
  • accession: MF193602
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus litorisediminis NBRC 112902GCA_009711205contigncbi2006130
66792Paracoccus litorisediminis strain NBRC 1129022006130.3wgspatric2006130

GC content

  • @ref: 65504
  • GC-content: 64.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno65.016yes
gram-positiveno98.222no
anaerobicno98.388no
aerobicyes91.623no
halophileno88.18no
spore-formingno96.513yes
glucose-utilyes94.336yes
flagellatedno87.871yes
thermophileno98.539no
glucose-fermentno86.805no

External links

@ref: 65504

culture collection no.: KCTC 52978, NBRC 112902

literature

  • topic: Phylogeny
  • Pubmed-ID: 28984555
  • title: Paracoccus litorisediminis sp. nov., isolated from a tidal flat.
  • authors: Park S, Choi J, Choi SJ, Yoon JH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002373
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
65504Sooyeon Park, Jeehyun Choi, Su Jung Choi and Jung-Hoon YoonParacoccus litorisediminis sp. nov., isolated from a tidal flat10.1099/ijsem.0.002373IJSEM 67: 4760-4766 201728984555
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
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.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