Strain identifier

BacDive ID: 131376

Type strain: Yes

Species: Chryseobacterium profundimaris

Strain Designation: DY46

Strain history: Y.-Y. Huo DY46.

NCBI tax ID(s): 1387275 (species)

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

@ref: 22603

BacDive-ID: 131376

DSM-Number: 28214

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Chryseobacterium profundimaris DY46 is a mesophilic bacterium that was isolated from deep-sea sediment.

NCBI tax id

  • NCBI tax id: 1387275
  • Matching level: species

strain history

@refhistory
22603<- L. Xu, Second Inst. Oceanography, State Oceanic Admin., Hangzhou, China; DY46 <- Y.-H. Wu
67770Y.-Y. Huo DY46.

doi: 10.13145/bacdive131376.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Chryseobacterium
  • species: Chryseobacterium profundimaris
  • full scientific name: Chryseobacterium profundimaris Xu et al. 2015

@ref: 22603

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium profundimaris

full scientific name: Chryseobacterium profundimaris Xu et al. 2015

strain designation: DY46

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 22603
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
22603positivegrowth28mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: MK-6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitude
22603deep-sea sedimentmid-ridge (33.11° W 5.96° N, at a depth of 2577 m)5.96-33.11
67770Deep-sea sediment sample collected from the Atlantic Ocean

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_3200.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_869;97_1017;98_2453;99_3200&stattab=map
  • Last taxonomy: Chryseobacterium
  • 16S sequence: KF434119
  • Sequence Identity:
  • Total samples: 420
  • soil counts: 32
  • aquatic counts: 63
  • animal counts: 276
  • plant counts: 49

Safety information

risk assessment

  • @ref: 22603
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22603
  • description: Chryseobacterium profundimaris strain DY46 16S ribosomal RNA gene, partial sequence
  • accession: KF434119
  • length: 1439
  • database: ena
  • NCBI tax ID: 1387275

Genome sequences

  • @ref: 66792
  • description: Chryseobacterium profundimaris DSM 28214
  • accession: 2724679817
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1387275

GC content

  • @ref: 22603
  • GC-content: 40.7
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 22603

culture collection no.: DSM 28214, CGMCC 1.12663, JCM 19801

straininfo link

  • @ref: 89813
  • straininfo: 397928

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25616910Chryseobacterium profundimaris sp. nov., a new member of the family Flavobacteriaceae isolated from deep-sea sediment.Xu L, Huo YY, Li ZY, Wang CS, Oren A, Xu XWAntonie Van Leeuwenhoek10.1007/s10482-015-0390-x2015Aerobiosis, Atlantic Ocean, Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/*isolation & purification/physiology, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Locomotion, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Phylogeny27902299Chryseobacterium nepalense sp. nov., isolated from oil-contaminated soil.Chaudhary DK, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0016802017Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nepal, Nucleic Acid Hybridization, *Petroleum Pollution, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogue
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
22603Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28214Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28214)
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
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/
89813Reimer, 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-ID397928.1