Workshop and Q&A October 6th

Strain identifier

BacDive ID: 24008

Type strain: Yes

Species: Ferrimonas sediminum

Strain Designation: JYr13

Strain history: X.-H. Zhang <-- R. Zhao JYr13.

NCBI tax ID(s): 718193 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
version 7 (current version):
version 6:
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version 4.1:
version 4:
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version 1:
version 7 (current version)


@ref: 20561

BacDive-ID: 24008

DSM-Number: 23317

keywords: Gram-negative, psychrophilic, facultative anaerobe, Bacteria, 16S sequence, genome sequence, motile, rod-shaped

description: Ferrimonas sediminum JYr13 is a facultative anaerobe, psychrophilic, Gram-negative bacterium that was isolated from coastal sediment of an amphioxus breeding zone.

NCBI tax id

  • NCBI tax id: 718193
  • Matching level: species

strain history

doi: 10.13145/bacdive24008.20220920.7

Name and taxonomic classification


  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Ferrimonadaceae
  • genus: Ferrimonas
  • species: Ferrimonas sediminum
  • full scientific name: Ferrimonas sediminum Ji et al. 2013

@ref: 20561

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Ferrimonadaceae

genus: Ferrimonas

species: Ferrimonas sediminum

full scientific name: Ferrimonas sediminum Ji et al. 2013

strain designation: JYr13

type strain: yes


cell morphology

  • @ref: 30700
  • gram stain: negative
  • cell length: 1.35 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: yes


  • @ref: 30700
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20561
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link:
  • 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


culture pH


Physiology and metabolism

oxygen tolerance

  • @ref: 30700
  • oxygen tolerance: facultative anaerobe


  • @ref: 30700
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 3 %


  • @ref: 67770
  • observation: quinones: MK-7, Q-7, Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3070016449alanine+carbon source
3070029987glutamate+carbon source
3070017596inosine+carbon source
3070024996lactate+carbon source
3070017748thymidine+carbon source
3070053423tween 40+carbon source
3070053426tween 80+carbon source
3070016704uridine+carbon source

metabolite production

  • @ref: 30700
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes


30700cytochrome oxidase+

Isolation, sampling and environmental information


@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
20561coastal sediment of an amphioxus breeding zoneQingdao, China (36° 5' N 120° 32' E)ChinaCHNAsia36.0833120.533
67770Coastal sediment of an amphioxus breeding zone in QingdaoChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 20561
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20561
  • description: Ferrimonas sediminum strain JYr13 16S ribosomal RNA gene, partial sequence
  • accession: GU391222
  • length: 1416
  • database: ena
  • NCBI tax ID: 718193

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ferrimonas sediminum DSM 23317GCA_900100175scaffoldncbi718193
66792Ferrimonas sediminum strain DSM 23317718193.3wgspatric718193
66792Ferrimonas sediminum DSM 233172634166324draftimg718193

GC content

2056159high performance liquid chromatography (HPLC)

External links

@ref: 20561

culture collection no.: DSM 23317, LMG 25564, JCM 17552

straininfo link



  • topic: Phylogeny
  • Pubmed-ID: 22685103
  • title: Ferrimonas sediminum sp. nov., isolated from coastal sediment of an amphioxus breeding zone.
  • authors: Ji S, Zhao R, Li Z, Li B, Shi X, Zhang XH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.042408-0
  • year: 2012
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, China, Chordata, DNA, Bacterial/genetics, Fatty Acids/analysis, Ferric Compounds/metabolism, Gammaproteobacteria/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA
  • topic2: Genetics


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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
20561Curators of the DSMZ Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23317)
30700Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172877604127031
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)
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 JCM