Strain identifier

BacDive ID: 13728

Type strain: Yes

Species: Paracoccus saliphilus

Strain history: <- S.-K. Tang and Y. Wang, YIM; YIM 90738 <- S.-K. Tang, Y. Wang et al.

NCBI tax ID(s): 405559 (species)

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General

@ref: 7476

BacDive-ID: 13728

DSM-Number: 18447

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

description: Paracoccus saliphilus DSM 18447 is an aerobe, Gram-negative, coccus-shaped bacterium that was isolated from saline-alkali soil.

NCBI tax id

  • NCBI tax id: 405559
  • Matching level: species

strain history

  • @ref: 7476
  • history: <- S.-K. Tang and Y. Wang, YIM; YIM 90738 <- S.-K. Tang, Y. Wang et al.

doi: 10.13145/bacdive13728.20240916.9.1

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 saliphilus
  • full scientific name: Paracoccus saliphilus Wang et al. 2009

@ref: 7476

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus saliphilus

full scientific name: Paracoccus saliphilus Wang et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29088negative4 µm1.8 µmcoccus-shapedno
69480negative97

pigmentation

  • @ref: 29088
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7476
  • name: ISP MEDIUM 2 WITH 5% NaCl (DSMZ Medium 636)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/636
  • composition: Name: ISP MEDIUM 2 WITH 5% NaCl (DSMZ Medium 636) Composition: NaCl 50.0 g/l Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
7476positivegrowth37
29088positivegrowth10-55
29088positiveoptimum37

culture pH

@refabilitytypepH
29088positivegrowth6.0-8.0
29088positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29088
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29088no
69480no90.969

halophily

@refsaltgrowthtested relationconcentration
29088NaClpositivegrowth1.0-15 %
29088NaClpositiveoptimum8 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2908830089acetate+carbon source
2908815963ribitol+carbon source
2908821217L-alaninamide+carbon source
2908816449alanine+carbon source
2908840585alpha-cyclodextrin+carbon source
2908822599arabinose+carbon source
2908818403L-arabitol+carbon source
2908822653asparagine+carbon source
2908835391aspartate+carbon source
2908817126DL-carnitine+carbon source
2908816947citrate+carbon source
2908815740formate+carbon source
2908828757fructose+carbon source
2908833984fucose+carbon source
2908828260galactose+carbon source
2908824175galacturonate+carbon source
2908824265gluconate+carbon source
2908817234glucose+carbon source
2908829987glutamate+carbon source
2908817754glycerol+carbon source
2908828087glycogen+carbon source
2908827570histidine+carbon source
29088182404-hydroxy-L-proline+carbon source
2908817596inosine+carbon source
2908824996lactate+carbon source
2908817716lactose+carbon source
2908825017leucine+carbon source
2908837684mannose+carbon source
2908828053melibiose+carbon source
2908851850methyl pyruvate+carbon source
2908818257ornithine+carbon source
2908850048phenylethylamine+carbon source
2908826271proline+carbon source
2908817148putrescine+carbon source
2908826490quinate+carbon source
2908817822serine+carbon source
2908830911sorbitol+carbon source
2908830031succinate+carbon source
2908817992sucrose+carbon source
2908826986threonine+carbon source
2908817748thymidine+carbon source
2908816704uridine+carbon source
2908827248urocanic acid+carbon source
2908817151xylitol+carbon source
290884853esculin+hydrolysis

enzymes

@refvalueactivityec
29088acid phosphatase+3.1.3.2
29088alkaline phosphatase+3.1.3.1
29088catalase+1.11.1.6
29088gelatinase+
29088cytochrome oxidase+1.9.3.1
29088urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 7476
  • sample type: saline-alkali soil
  • geographic location: Xinjiang province, edge of Ebinur Lake wetland natural reserve
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Alkaline
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_3628.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1884;97_2262;98_2776;99_3628&stattab=map
  • Last taxonomy: Paracoccus
  • 16S sequence: DQ923133
  • Sequence Identity:
  • Total samples: 176
  • soil counts: 31
  • aquatic counts: 124
  • animal counts: 19
  • plant counts: 2

Safety information

risk assessment

  • @ref: 7476
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7476
  • description: Paracoccus saliphilus strain YIM 90738 16S ribosomal RNA gene, partial sequence
  • accession: DQ923133
  • length: 1389
  • database: nuccore
  • NCBI tax ID: 405559

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus saliphilus strain DSM 18447405559.3wgspatric405559
66792Paracoccus saliphilus DSM 184472681813562draftimg405559
66792Paracoccus saliphilus DSM 18447GCA_028553805completencbi405559

GC content

@refGC-contentmethod
747660.3high performance liquid chromatography (HPLC)
2908860.3

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno97yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.81yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes81.371yes
69480spore-formingspore-formingAbility to form endo- or exosporesno90.969yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno99.279no
69480flagellatedmotile2+Ability to perform flagellated movementno56.739no

External links

@ref: 7476

culture collection no.: DSM 18447, CCTCC AB 206074, KCTC 22163, YIM 90738

straininfo link

  • @ref: 82911
  • straininfo: 402335

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19567556Paracoccus saliphilus sp. nov., a halophilic bacterium isolated from a saline soil.Wang Y, Tang SK, Lou K, Mao PH, Jin X, Jiang CL, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.005918-02009Bacterial Typing Techniques, Base Composition, Benzoquinones/analysis, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics
Phylogeny32039746Paracoccus alkanivorans sp. nov., isolated from a deep well with oil reservoir water.Zhang YX, Li X, Li FL, Ma SC, Zheng GD, Chen WF, Li WJ, Wang LInt J Syst Evol Microbiol10.1099/ijsem.0.0040362020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oil and Gas Fields/*microbiology, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry, *Water MicrobiologyTranscriptome
Phylogeny34388083Paracoccus onubensis sp. nov., a novel alphaproteobacterium isolated from the wall of a show cave.Gutierrez-Patricio S, Gonzalez-Pimentel JL, Miller AZ, Hermosin B, Saiz-Jimenez C, Jurado VInt J Syst Evol Microbiol10.1099/ijsem.0.0049422021Bacterial Typing Techniques, Base Composition, Caves/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Paracoccus/classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7476Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18447)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18447
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
29088Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2551728776041
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)
82911Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402335.1StrainInfo: A central database for resolving microbial strain identifiers