Strain identifier

BacDive ID: 24492

Type strain: Yes

Species: Paracoccus siganidrum

Strain Designation: M26

Strain history: <- Y. Liu, Guangdong Ocean Univ., College of Food Science and Technol., China; M26 <- W. Shi

NCBI tax ID(s): 1276757 (species)

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General

@ref: 20720

BacDive-ID: 24492

DSM-Number: 26381

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Paracoccus siganidrum M26 is a mesophilic, Gram-negative bacterium that was isolated from gastrointestinal tract of the fish Siganus fuscescens.

NCBI tax id

  • NCBI tax id: 1276757
  • Matching level: species

strain history

  • @ref: 20720
  • history: <- Y. Liu, Guangdong Ocean Univ., College of Food Science and Technol., China; M26 <- W. Shi

doi: 10.13145/bacdive24492.20230509.8.1

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 siganidrum
  • full scientific name: Paracoccus siganidrum Liu et al. 2013

@ref: 20720

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus siganidrum

full scientific name: Paracoccus siganidrum Liu et al. 2013

strain designation: M26

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.994

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20720TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
20720CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water

culture temp

  • @ref: 20720
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.995

Isolation, sampling and environmental information

isolation

  • @ref: 20720
  • sample type: gastrointestinal tract of the fish Siganus fuscescens
  • host species: Siganus fuscescens
  • geographic location: Guangdong province, Zhanjiang port (N21° 9', E110°17')
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 21.15
  • longitude: 110.283

isolation source categories

Cat1Cat2
#Host#Fishes
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_38941.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_529;97_12974;98_28523;99_38941&stattab=map
  • Last taxonomy: Paracoccus siganidrum
  • 16S sequence: JX398976
  • Sequence Identity:
  • Total samples: 120
  • soil counts: 15
  • aquatic counts: 66
  • animal counts: 37
  • plant counts: 2

Sequence information

16S sequences

  • @ref: 20720
  • description: Paracoccus siganidrum strain M26 16S ribosomal RNA gene, partial sequence
  • accession: JX398976
  • length: 1422
  • database: ena
  • NCBI tax ID: 1276757

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus siganidrum M26GCA_003709565contigncbi1276757
66792Paracoccus siganidrum DSM 26381GCA_003594835contigncbi1276757
66792Paracoccus siganidrum strain DSM 263811276757.3wgspatric1276757
66792Paracoccus siganidrum M262834594880draftimg1276757

GC content

  • @ref: 20720
  • GC-content: 64.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno86no
motileno72.374no
gram-positiveno98.119no
anaerobicno98.791no
aerobicyes92.548no
halophileno77.388no
spore-formingno96.213no
thermophileno96.708no
glucose-utilyes88.782no
flagellatedno89.693no
glucose-fermentno85.544no

External links

@ref: 20720

culture collection no.: DSM 26381, CCTCC AB 2012865

literature

  • topic: Phylogeny
  • Pubmed-ID: 23546859
  • title: Paracoccus siganidrum sp. nov., isolated from fish gastrointestinal tract.
  • authors: Liu Y, Xie QY, Hong K, Li L, Zhao YM, Tang YL, An JY, Zhu PP, Xu CH
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-013-9894-4
  • year: 2013
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fishes/*microbiology, Gastrointestinal Tract/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/*isolation & purification/physiology, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
20720Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26381Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26381)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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