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)

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General

@ref: 16210

BacDive-ID: 13729

DSM-Number: 22220

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

description: Paracoccus isoporae SW-3 is an aerobe, Gram-negative, motile 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/bacdive13729.20240916.9.1

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
69480negative97.994

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

@refgrowthtypetemperature
16210positivegrowth25
29870positivegrowth04-40
29870positiveoptimum27.5

culture pH

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

Physiology and metabolism

oxygen tolerance

  • @ref: 29870
  • oxygen tolerance: aerobe

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, Province of China
  • 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: nuccore
  • 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

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno72no
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.994yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.248yes
69480spore-formingspore-formingAbility to form endo- or exosporesno89.84no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.322yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.821yes
69480flagellatedmotile2+Ability to perform flagellated movementyes64.389no

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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
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