Strain identifier

BacDive ID: 14299

Type strain: Yes

Species: Parasphingopyxis lamellibrachiae

Strain history: M. Miyazaki JAMH 0132.

NCBI tax ID(s): 680125 (species)

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General

@ref: 18275

BacDive-ID: 14299

DSM-Number: 26725

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

description: Parasphingopyxis lamellibrachiae DSM 26725 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Trophosome of annelid worm Lamellibrachia satsuma.

NCBI tax id

  • NCBI tax id: 680125
  • Matching level: species

strain history

@refhistory
18275<- Y. Nogi, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Extremobiosphere Res. Center, Yokosuka
67770M. Miyazaki JAMH 0132.

doi: 10.13145/bacdive14299.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Parasphingopyxis
  • species: Parasphingopyxis lamellibrachiae
  • full scientific name: Parasphingopyxis lamellibrachiae Uchida et al. 2012

@ref: 18275

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Parasphingopyxis

species: Parasphingopyxis lamellibrachiae

full scientific name: Parasphingopyxis lamellibrachiae Uchida et al. 2012

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30347negative1.5 µm0.55 µmrod-shapedyes
69480negative99.981

colony morphology

  • @ref: 18275
  • incubation period: 2-3 days

pigmentation

  • @ref: 30347
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 18275
  • 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
18275positivegrowth28mesophilic
30347positivegrowth05-36
30347positiveoptimum29mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30347positivegrowth6-9.5alkaliphile
30347positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30347
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30347no
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
30347NaClpositivegrowth0.5-5 %
30347NaClpositiveoptimum2 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3034722599arabinose+carbon source
3034717234glucose+carbon source
3034717632nitrate+reduction
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
30347gelatinase+
30347cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
18275+-------------------+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
18275Trophosome of annelid worm Lamellibrachia satsumaLamellibrachia satsumaKagoshima BayJapanJPNAsia
67770Trophosome of a tubeworm (Lamellibrachia satsuma) in Kagoshima BayLamellibrachia satsumaJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Annelida
#Host Body-Site#Organ

taxonmaps

  • @ref: 69479
  • File name: preview.99_18950.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_9665;97_11646;98_14317;99_18950&stattab=map
  • Last taxonomy: Parasphingopyxis lamellibrachiae subclade
  • 16S sequence: AB524074
  • Sequence Identity:
  • Total samples: 2208
  • soil counts: 190
  • aquatic counts: 1886
  • animal counts: 86
  • plant counts: 46

Safety information

risk assessment

  • @ref: 18275
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18275
  • description: Parasphingopyxis lamellibrachiae gene for 16S ribosomal RNA, partial sequence
  • accession: AB524074
  • length: 1447
  • database: ena
  • NCBI tax ID: 680125

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parasphingopyxis lamellibrachiae strain DSM 26725680125.3wgspatric680125
66792Parasphingopyxis lamellibrachiae DSM 267252770939550draftimg680125
67770Parasphingopyxis lamellibrachiae DSM 26725GCA_003385775scaffoldncbi680125

GC content

@refGC-contentmethod
3034760.1
6777060.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.817no
anaerobicno99.343no
halophileno84.109no
spore-formingno97.305yes
glucose-utilyes60.906no
flagellatedno96.103no
thermophileno94.368yes
motileno86.108no
aerobicyes94.41yes
glucose-fermentno91.875no

External links

@ref: 18275

culture collection no.: DSM 26725, JCM 15549, NCIMB 14486, JAMH 0132

straininfo link

  • @ref: 83452
  • straininfo: 401434

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22081711Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm.Uchida H, Hamana K, Miyazaki M, Yoshida T, Nogi YInt J Syst Evol Microbiol10.1099/ijs.0.034033-02011Animals, Annelida/*microbiology, Base Composition, Bays, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purificationGenetics
Phylogeny28884660Parasphingopyxis algicola sp. nov., isolated from a marine red alga Asparagopsis taxiformis and emended description of the genus Parasphingopyxis Uchida et al. 2012.Jeong SE, Kim KH, Baek K, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0022152017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodophyta/*microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny34633920Parasphingopyxis marina sp. nov. isolated from coastal seawater.Choi SY, Oh JS, Roh DHInt J Syst Evol Microbiol10.1099/ijsem.0.0050492021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Seawater/microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
18275Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26725)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26725
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
30347Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2668828776041
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
83452Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401434.1StrainInfo: A central database for resolving microbial strain identifiers