Strain identifier

BacDive ID: 134305

Type strain: Yes

Species: Actibacter sediminis

Strain Designation: JC2129

Strain history: <- J Chun, Seoul Univ.

NCBI tax ID(s): 449463 (species)

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General

@ref: 32340

BacDive-ID: 134305

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

description: Actibacter sediminis JC2129 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 449463
  • Matching level: species

strain history

@refhistory
67770J. Chun JC2129.
67771<- J Chun, Seoul Univ.

doi: 10.13145/bacdive134305.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Actibacter
  • species: Actibacter sediminis
  • full scientific name: Actibacter sediminis Kim et al. 2008

@ref: 32340

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Actibacter

species: Actibacter sediminis

strain designation: JC2129

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32340negative2.8 µm0.8 µmrod-shapedno
67771rod-shapedno
67771negative

pigmentation

  • @ref: 32340
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
32340positivegrowth05-45
32340positiveoptimum37mesophilic
67770positivegrowth30mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepH
32340positivegrowth05-08
32340positiveoptimum6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32340aerobe
67771aerobe

spore formation

  • @ref: 32340
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32340NaClpositivegrowth01-10 %
32340NaClpositiveoptimum2 %

observation

@refobservation
67770quinones: MK-6, MK-7
67771quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3234030089acetate+carbon source
3234016947citrate+carbon source
3234029987glutamate+carbon source
3234015361pyruvate+carbon source
3234017992sucrose+carbon source
323404853esculin+hydrolysis

enzymes

@refvalueactivityec
32340acid phosphatase+3.1.3.2
32340alkaline phosphatase+3.1.3.1
32340catalase+1.11.1.6
32340gelatinase+
32340cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
32340marine sediment
67770Tidal flat sediment of Dongmak on Ganghwa IslandRepublic of KoreaKORAsia
67771From sediment of getbol(a Korean word for tidal flat)Republic of KoreaKORAsiaDongmak, Ganghwa Island

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_102518.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1049;96_12459;97_15129;98_56929;99_102518&stattab=map
  • Last taxonomy: Actibacter
  • 16S sequence: EF670651
  • Sequence Identity:
  • Total samples: 4854
  • soil counts: 60
  • aquatic counts: 4687
  • animal counts: 75
  • plant counts: 32

Sequence information

16S sequences

  • @ref: 32340
  • description: Actibacter sediminis strain JC2129 16S ribosomal RNA gene, partial sequence
  • accession: EF670651
  • length: 1374
  • database: nuccore
  • NCBI tax ID: 449463

GC content

@refGC-contentmethod
3234043-45
6777043-45high performance liquid chromatography (HPLC)
6777143.0-45.0

External links

@ref: 32340

culture collection no.: KCTC 12704, JCM 14002

literature

  • topic: Phylogeny
  • Pubmed-ID: 18175699
  • title: Actibacter sediminis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment.
  • authors: Kim JH, Kim KY, Hahm YT, Kim BS, Chun J, Cha CJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65346-0
  • year: 2008
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Flavobacteriaceae/chemistry/classification/genetics/*isolation & purification, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity
  • topic2: Genetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
32340Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172857228776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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/