Strain identifier

BacDive ID: 7258

Type strain: Yes

Species: Agrococcus jejuensis

Strain Designation: SSW1-48

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 399736 (species)

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General

@ref: 16094

BacDive-ID: 7258

DSM-Number: 22002

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped

description: Agrococcus jejuensis SSW1-48 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Dried seaweed.

NCBI tax id

  • NCBI tax id: 399736
  • Matching level: species

strain history

@refhistory
16094<- JCM/RIKEN <- S. D. Lee, Cheju National Univ., Rep. of Korea; SSW1-48
67770S. D. Lee SSW1-48.
67771<- SD Lee, Cheju Univ.

doi: 10.13145/bacdive7258.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agrococcus
  • species: Agrococcus jejuensis
  • full scientific name: Agrococcus jejuensis Lee 2008

@ref: 16094

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agrococcus

species: Agrococcus jejuensis

full scientific name: Agrococcus jejuensis Lee 2008

strain designation: SSW1-48

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32585positive1.3-1.5 µm0.3-0.4 µmrod-shapedno
67771positive
69480positive100

pigmentation

  • @ref: 32585
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16094
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16094positivegrowth28mesophilic
32585positivegrowth10-37
32585positiveoptimum30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32585positivegrowth6.1-12.1alkaliphile
32585positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32585aerobe
67771aerobe

spore formation

@refspore formationconfidence
32585no
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
32585NaClpositivegrowth0-3 %
32585NaClpositiveoptimum0-3 %

observation

@refobservation
32585aggregates in chains
67770quinones: MK-10, MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3258517234glucose+carbon source
3258525115malate+carbon source
3258517306maltose+carbon source
3258529864mannitol+carbon source
3258537684mannose+carbon source
32585506227N-acetylglucosamine+carbon source

enzymes

  • @ref: 32585
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16094Dried seaweedJeju, Samyang BeachRepublic of KoreaKORAsia
67770Dried seaweed around Samyang Beach in JejuRepublic of KoreaKORAsia
67771From seaweedJejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2
#Host#Algae
#Engineered#Food production
#Condition#Xerophilic

Safety information

risk assessment

  • @ref: 16094
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16094
  • description: Phycibacter jejuensis partial 16S rRNA gene, type strain SSW1-48T
  • accession: AM396260
  • length: 1415
  • database: ena
  • NCBI tax ID: 399736

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agrococcus jejuensis DSM 22002GCA_900099705chromosomencbi399736
66792Agrococcus jejuensis strain DSM 22002399736.3completepatric399736
66792Agrococcus jejuensis DSM 220022634166279draftimg399736

GC content

@refGC-contentmethod
1609473.0high performance liquid chromatography (HPLC)
3258573
6777073high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes92.78yes
anaerobicno99.503yes
halophileno91.521no
spore-formingno95.165no
glucose-utilyes85.112yes
aerobicyes95.091yes
motileno89.105yes
flagellatedno96.743yes
thermophileno99.679no
glucose-fermentno88.762no

External links

@ref: 16094

culture collection no.: DSM 22002, JCM 14256, KCTC 19198

straininfo link

  • @ref: 76710
  • straininfo: 402243

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18842844Agrococcus jejuensis sp. nov., isolated from dried seaweed.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.65731-02008Actinomycetales/chemistry/*classification/*genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids, Genes, Bacterial, Genes, rRNA, Korea, Molecular Sequence Data, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Seaweed/*microbiology, Vitamin K 2/chemistryGenetics
Phylogeny19783614Agrococcus terreus sp. nov. and Micrococcus terreus sp. nov., isolated from forest soil.Zhang JY, Liu XY, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.013235-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Micrococcaceae/*classification/genetics/*isolation & purification/metabolism, Micrococcus/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16094Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22002)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22002
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32585Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2880028776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically 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 Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76710Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402243.1StrainInfo: A central database for resolving microbial strain identifiers