Strain identifier
BacDive ID: 132484
Type strain:
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)
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
@ref | name | growth | link | composition |
---|---|---|---|---|
43993 | Marine agar (MA) | yes | ||
24273 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
43993 | positive | growth | 10-25 | |
43993 | positive | optimum | 20 | psychrophilic |
24273 | positive | growth | 20 | psychrophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
43993 | positive | growth | 6.0-9.0 | alkaliphile |
43993 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 43993
- oxygen tolerance: aerobe
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43993 | NaCl | positive | growth | 0-8 %(w/v) |
43993 | NaCl | positive | optimum | 1 %(w/v) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43993 | 30916 | 2-oxoglutarate | + | energy source |
43993 | 30089 | acetate | + | energy source |
43993 | 16335 | adenosine | + | energy source |
43993 | 17925 | alpha-D-glucose | + | energy source |
43993 | 16027 | amp | + | energy source |
43993 | 17057 | cellobiose | + | energy source |
43993 | 15824 | D-fructose | + | energy source |
43993 | 8391 | D-gluconate | + | energy source |
43993 | 16024 | D-mannose | + | energy source |
43993 | 16724 | 4-hydroxybutyrate | + | energy source |
43993 | 17754 | glycerol | + | energy source |
43993 | 17596 | inosine | + | energy source |
43993 | 75144 | lactamide | + | energy source |
43993 | maltose hydrate | + | energy source | |
43993 | 61993 | maltotriose | + | energy source |
43993 | 75146 | monomethyl succinate | + | energy source |
43993 | 44337 | N-acetyl-L-glutamate | + | energy source |
43993 | 18394 | palatinose | + | energy source |
43993 | 17272 | propionate | + | energy source |
43993 | 15361 | pyruvate | + | energy source |
43993 | 143136 | succinamate | + | energy source |
43993 | 17992 | sucrose | + | energy source |
43993 | 32528 | turanose | + | energy source |
43993 | 53426 | tween 80 | + | energy source |
43993 | 16704 | uridine | + | energy source |
43993 | 17634 | D-glucose | + | fermentation |
43993 | 16199 | urea | + | fermentation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43993 | catalase | + | 1.11.1.6 |
43993 | cytochrome oxidase | + | 1.9.3.1 |
43993 | esterase (C 4) | + | |
43993 | esterase Lipase (C 8) | + | |
43993 | leucine arylamidase | + | 3.4.11.1 |
43993 | valine arylamidase | + | |
43993 | trypsin | + | 3.4.21.4 |
43993 | acid phosphatase | + | 3.1.3.2 |
43993 | naphthol-AS-BI-phosphohydrolase | + | |
43993 | alpha-glucosidase | + | 3.2.1.20 |
fatty acid profile
fatty acids
@ref fatty acid percentage 43993 C15:0 anteiso 46.9 43993 C17:0 anteiso 13.6 43993 C17:1 anteiso ω9c 0.7 43993 C16:0 0.9 43993 C16:1ω7c / C16:1ω6c 575 43993 C14:0 iso 0.5 43993 C15:0 iso 25.9 43993 C16:0 iso 2.9 43993 C17:0 iso 5.8 43993 C17:1 iso ω9c / C16:0 10-methyl 225 - 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
@ref | sample type | host species | geographic location | country | origin.country | continent | enrichment culture | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|---|
24273 | gut of a purple sea urchin, Heliocidaris crassispina | Heliocidaris crassispina | Dokdo island, coastal waters | Republic of Korea | KOR | Asia | |||
43993 | gut of a purple sea urchin Heliocidaris crassispina collected from the coastal waters of the Korean island Dokdo | Dokdo | Republic of Korea | KOR | Asia | Marine agar 2216 | 7 days | 25 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Arthrobacter echini AM23 | GCA_004803505 | contig | ncbi | 1529066 |
66792 | Arthrobacter echini AM23 | 2903061041 | draft | img | 1529066 |
GC content
@ref | GC-content | method |
---|---|---|
43993 | 67.3 | real time PCR (RTD-PCR) |
24273 | 67.3 | fluorimetric |
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
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
24273 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29493 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29493) | |||
43993 | June-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 Bae | Arthrobacter echini sp. nov., isolated from the gut of a purple sea urchin, Heliocidaris crassispina | 10.1099/ijsem.0.000965 | IJSEM 66: 1887-1893 2016 | 26868361 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
90815 | Reimer, 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 identifiers | 10.60712/SI-ID400295.1 |