Strain identifier

BacDive ID: 13729

Type strain: Yes

Species: Paracoccus isoporae

Strain Designation: SW-3

Strain history: <- J.-H. Chou, Natl. Kaohsiung Marine Univ. Taiwan <- W.-M. Chen; SW-3

NCBI tax ID(s): 591205 (species)

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

@ref: 16210

BacDive-ID: 13729

DSM-Number: 22220

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

description: Paracoccus isoporae SW-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from reef-building coral Isopora palifera.

NCBI tax id

  • NCBI tax id: 591205
  • Matching level: species

strain history

  • @ref: 16210
  • history: <- J.-H. Chou, Natl. Kaohsiung Marine Univ. Taiwan <- W.-M. Chen; SW-3

doi: 10.13145/bacdive13729.20230509.8.1

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 isoporae
  • full scientific name: Paracoccus isoporae Chen et al. 2011

@ref: 16210

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus isoporae

full scientific name: Paracoccus isoporae Chen et al. 2011

strain designation: SW-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29870negative1.1 µm0.6 µmrod-shapedyes
69480negative99.995

Culture and growth conditions

culture medium

  • @ref: 16210
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16210positivegrowth25mesophilic
29870positivegrowth04-40
29870positiveoptimum27.5mesophilic

culture pH

@refabilitytypepHPH range
29870positivegrowth07-10alkaliphile
29870positiveoptimum9.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29870
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.997

halophily

@refsaltgrowthtested relationconcentration
29870NaClpositivegrowth0-12 %
29870NaClpositiveoptimum4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29870620642,3-butanediol+carbon source
2987033984fucose+carbon source
2987028260galactose+carbon source
2987017234glucose+carbon source
2987017754glycerol+carbon source
2987017716lactose+carbon source
2987017306maltose+carbon source
2987029864mannitol+carbon source
2987051850methyl pyruvate+carbon source
2987017992sucrose+carbon source
2987027082trehalose+carbon source
2987053424tween 20+carbon source
2987053423tween 40+carbon source
2987053425tween 60+carbon source
2987053426tween 80+carbon source
298704853esculin+hydrolysis

enzymes

@refvalueactivityec
29870acid phosphatase+3.1.3.2
29870alkaline phosphatase+3.1.3.1
29870alpha-galactosidase+3.2.1.22
29870catalase+1.11.1.6
29870cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 16210
  • sample type: reef-building coral Isopora palifera
  • host species: Isopora palifera
  • geographic location: Pingtung County, off the coast of Kenting (21°56' 29'' N 120° 44' 70'' E)
  • country: Taiwan
  • origin.country: TWN
  • continent: Asia

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Cnidaria (Corals)

taxonmaps

  • @ref: 69479
  • File name: preview.99_174209.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_33499;97_42467;98_114056;99_174209&stattab=map
  • Last taxonomy: Paracoccus isoporae subclade
  • 16S sequence: FJ593906
  • Sequence Identity:
  • Total samples: 67
  • soil counts: 3
  • aquatic counts: 37
  • animal counts: 27

Safety information

risk assessment

  • @ref: 16210
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16210
  • description: Paracoccus isoporae strain SW-3 16S ribosomal RNA gene, partial sequence
  • accession: FJ593906
  • length: 1426
  • database: ena
  • NCBI tax ID: 591205

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus isoporae DSM 22220GCA_900101865contigncbi591205
66792Paracoccus isoporae strain DSM 22220591205.3wgspatric591205
66792Paracoccus isoporae DSM 222202675903152draftimg591205

GC content

  • @ref: 16210
  • GC-content: 63.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno72no
gram-positiveno97.433no
anaerobicno98.954yes
halophileyes55.783no
spore-formingno96.913no
glucose-utilyes87.351yes
flagellatedno83.842no
aerobicyes92.78yes
thermophileno93.513yes
motileyes65.895yes
glucose-fermentno91.997no

External links

@ref: 16210

culture collection no.: DSM 22220, BCRC 17967, LMG 25205

straininfo link

  • @ref: 82912
  • straininfo: 360699

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20543151Paracoccus isoporae sp. nov., isolated from the reef-building coral Isopora palifera.Chen MH, Sheu SY, Chen CA, Wang JT, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.023333-02010Animals, Anthozoa/*microbiology, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Paracoccus/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, TaiwanMetabolism
Phylogeny32579093Paracoccus xiamenensis sp. nov., isolated from seawater on the Xiamen.Lyu L, Zhi B, Lai Q, Shao Z, Yu ZInt J Syst Evol Microbiol10.1099/ijsem.0.0042842020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16210Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22220)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22220
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
29870Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2624428776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic 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.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)
82912Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360699.1StrainInfo: A central database for resolving microbial strain identifiers