Strain identifier

BacDive ID: 131265

Type strain: Yes

Species: Croceibacterium atlanticum

Strain Designation: 26DY36

Strain history: Y.-H. Wu 26DY36.

NCBI tax ID(s): 1267766 (species)

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

@ref: 22492

BacDive-ID: 131265

DSM-Number: 100738

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

description: Croceibacterium atlanticum 26DY36 is a mesophilic, Gram-negative bacterium that was isolated from North Atlantic Rise.

NCBI tax id

  • NCBI tax id: 1267766
  • Matching level: species

strain history

@refhistory
22492<- Y.-H. Wu, Second Inst. Oceanography, State Oceanic Admin., Hangzhou, China; CGMCC 1.12411
67770Y.-H. Wu 26DY36.

doi: 10.13145/bacdive131265.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Croceibacterium
  • species: Croceibacterium atlanticum
  • full scientific name: Croceibacterium atlanticum (Wu et al. 2014) Xu et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Altererythrobacter atlanticus

@ref: 22492

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Altererythrobacter

species: Altererythrobacter atlanticus

full scientific name: Altererythrobacter atlanticus Wu et al. 2014

strain designation: 26DY36

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.854

Culture and growth conditions

culture medium

  • @ref: 22492
  • 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
22492positivegrowth28mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.984

observation

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

Isolation, sampling and environmental information

isolation

@refsample typecountry
22492North Atlantic RiseAtlantic Ocean
67770Deep-sea sediment sample collected from the North Atlantic Rise

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_3915.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_543;97_2405;98_2973;99_3915&stattab=map
  • Last taxonomy: Altererythrobacter atlanticus subclade
  • 16S sequence: KC018454
  • Sequence Identity:
  • Total samples: 996
  • soil counts: 342
  • aquatic counts: 364
  • animal counts: 264
  • plant counts: 26

Safety information

risk assessment

  • @ref: 22492
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22492
  • description: Altererythrobacter atlanticus strain 26DY36 16S ribosomal RNA gene, partial sequence
  • accession: KC018454
  • length: 1444
  • database: ena
  • NCBI tax ID: 1267766

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Croceibacterium atlanticum 26DY36GCA_001008165completencbi1267766
66792Croceibacterium atlanticum DSM 100738GCA_014199315scaffoldncbi1267766
66792Altererythrobacter atlanticus strain 26DY361267766.8plasmidpatric1267766
66792Altererythrobacter atlanticus strain 26DY361267766.3completepatric1267766
66792Altererythrobacter atlanticus strain DSM 1007381267766.10wgspatric1267766
66792Altererythrobacter atlanticus DSM 1007382828423711draftimg1267766

GC content

@refGC-contentmethod
6777061.9genome sequence analysis
6777059.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes65.722no
motileyes65.722no
flagellatedno88.377no
flagellatedno88.377no
gram-positiveno97.242no
gram-positiveno97.242no
anaerobicno97.888no
anaerobicno97.888no
aerobicyes87.769no
aerobicyes87.769no
halophileno78.947no
halophileno78.947no
spore-formingno95.129no
spore-formingno95.129no
thermophileno97.09no
thermophileno97.09no
glucose-utilyes78.97no
glucose-utilyes78.97no
glucose-fermentno93.056no
glucose-fermentno93.056no

External links

@ref: 22492

culture collection no.: DSM 100738, CGMCC 1.12411, JCM 18865

straininfo link

  • @ref: 89709
  • straininfo: 407893

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
22492Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100738Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100738)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89709Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID407893.1