Strain identifier

BacDive ID: 132484

Type strain: Yes

Species: Arthrobacter echini

Strain Designation: AM23

Strain history: <- J.-W. Bae, Kyung Hee Univ., Seoul, Republic of Korea; AM23 <- J. Y. Lee

NCBI tax ID(s): 1529066 (species)

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

@ref: 24273

BacDive-ID: 132484

DSM-Number: 29493

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, coccus-shaped, colony-forming

description: Arthrobacter echini AM23 is an aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from gut of a purple sea urchin, Heliocidaris crassispina.

NCBI tax id

  • NCBI tax id: 1529066
  • Matching level: species

strain history

  • @ref: 24273
  • history: <- J.-W. Bae, Kyung Hee Univ., Seoul, Republic of Korea; AM23 <- J. Y. Lee

doi: 10.13145/bacdive132484.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Arthrobacter
  • species: Arthrobacter echini
  • full scientific name: Arthrobacter echini Lee et al. 2016

@ref: 24273

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter echini

full scientific name: Arthrobacter echini Lee et al. 2016

strain designation: AM23

type strain: yes

Morphology

cell morphology

  • @ref: 43993
  • gram stain: positive
  • cell length: 1.2-2.2 µm
  • cell width: 1.2-2.2 µm
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 43993
  • colony size: 0.1-0.15 mm
  • colony color: dark pink
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Marine agar 2216

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43993Marine agar (MA)yes
24273BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
43993positivegrowth10-25
43993positiveoptimum20psychrophilic
24273positivegrowth20psychrophilic

culture pH

@refabilitytypepHPH range
43993positivegrowth6.0-9.0alkaliphile
43993positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43993
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
43993NaClpositivegrowth0-8 %(w/v)
43993NaClpositiveoptimum1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43993309162-oxoglutarate+energy source
4399330089acetate+energy source
4399316335adenosine+energy source
4399317925alpha-D-glucose+energy source
4399316027amp+energy source
4399317057cellobiose+energy source
4399315824D-fructose+energy source
439938391D-gluconate+energy source
4399316024D-mannose+energy source
43993167244-hydroxybutyrate+energy source
4399317754glycerol+energy source
4399317596inosine+energy source
4399375144lactamide+energy source
43993maltose hydrate+energy source
4399361993maltotriose+energy source
4399375146monomethyl succinate+energy source
4399344337N-acetyl-L-glutamate+energy source
4399318394palatinose+energy source
4399317272propionate+energy source
4399315361pyruvate+energy source
43993143136succinamate+energy source
4399317992sucrose+energy source
4399332528turanose+energy source
4399353426tween 80+energy source
4399316704uridine+energy source
4399317634D-glucose+fermentation
4399316199urea+fermentation

enzymes

@refvalueactivityec
43993catalase+1.11.1.6
43993cytochrome oxidase+1.9.3.1
43993esterase (C 4)+
43993esterase Lipase (C 8)+
43993leucine arylamidase+3.4.11.1
43993valine arylamidase+
43993trypsin+3.4.21.4
43993acid phosphatase+3.1.3.2
43993naphthol-AS-BI-phosphohydrolase+
43993alpha-glucosidase+3.2.1.20

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43993C15:0 anteiso46.9
    43993C17:0 anteiso13.6
    43993C17:1 anteiso ω9c0.7
    43993C16:00.9
    43993C16:1ω7c / C16:1ω6c575
    43993C14:0 iso0.5
    43993C15:0 iso25.9
    43993C16:0 iso2.9
    43993C17:0 iso5.8
    43993C17:1 iso ω9c / C16:0 10-methyl225
  • type of FA analysis: whole cell analysis
  • incubation medium: Marine agar 2216
  • agar/liquid: agar
  • incubation temperature: 20
  • incubation time: 3
  • software version: Sherlock 6.2
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Agilent 6890 gas chromatograph
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
24273gut of a purple sea urchin, Heliocidaris crassispinaHeliocidaris crassispinaDokdo island, coastal watersRepublic of KoreaKORAsia
43993gut of a purple sea urchin Heliocidaris crassispina collected from the coastal waters of the Korean island DokdoDokdoRepublic of KoreaKORAsiaMarine agar 22167 days25

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Host Body-Site#Gastrointestinal tract#Stomach
#Host#Invertebrates (Other)#Echinodermata
#Host Body-Site#Gastrointestinal tract

Safety information

risk assessment

  • @ref: 24273
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24273
  • description: Arthrobacter echini strain AM23 16S ribosomal RNA gene, partial sequence
  • accession: KJ789956
  • length: 1468
  • database: ena
  • NCBI tax ID: 1529066

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arthrobacter echini AM23GCA_004803505contigncbi1529066
66792Arthrobacter echini AM232903061041draftimg1529066

GC content

@refGC-contentmethod
4399367.3real time PCR (RTD-PCR)
2427367.3fluorimetric

External links

@ref: 24273

culture collection no.: DSM 29493, KACC 18260

straininfo link

  • @ref: 90815
  • straininfo: 400295

literature

  • topic: Phylogeny
  • Pubmed-ID: 26868361
  • title: Arthrobacter echini sp. nov., isolated from the gut of a purple sea urchin, Heliocidaris crassispina.
  • authors: Lee JY, Hyun DW, Soo Kim P, Sik Kim H, Shin NR, Yun JH, Jung MJ, Kim MS, Woong Whon T, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000965
  • year: 2016
  • mesh: Animals, Anthocidaris/*microbiology, Arthrobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/chemistry
  • topic2: Genetics

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
24273Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29493Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29493)
43993June-Young Lee, Dong-Wook Hyun, Pil Soo Kim, Hyun Sik Kim, Na-Ri Shin, Ji-Hyun Yun, Mi-Ja Jung, Min-Soo Kim, Tae Woong Whon, Jin-Woo BaeArthrobacter echini sp. nov., isolated from the gut of a purple sea urchin, Heliocidaris crassispina10.1099/ijsem.0.000965IJSEM 66: 1887-1893 201626868361
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
90815Reimer, 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-ID400295.1