Strain identifier

BacDive ID: 12671

Type strain: Yes

Species: Aestuariimicrobium kwangyangense

Strain Designation: R27

Strain history: CIP <- 2007, JCM <- 2006, J.H. Yoon, KRIBB, Taejon, Korea: strain R27

NCBI tax ID(s): 1120954 (strain), 396389 (species)

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General

@ref: 15788

BacDive-ID: 12671

DSM-Number: 21549

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

description: Aestuariimicrobium kwangyangense R27 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from oil-contaminated tidal flat sediment.

NCBI tax id

NCBI tax idMatching level
396389species
1120954strain

strain history

@refhistory
15788<- JCM <- J.-H. Yoon; R27
67770J.-H. Yoon R27.
67771<- JH Yoon, KRIBB
120520CIP <- 2007, JCM <- 2006, J.H. Yoon, KRIBB, Taejon, Korea: strain R27

doi: 10.13145/bacdive12671.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Propionibacteriaceae
  • genus: Aestuariimicrobium
  • species: Aestuariimicrobium kwangyangense
  • full scientific name: Aestuariimicrobium kwangyangense Jung et al. 2007

@ref: 15788

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Aestuariimicrobium

species: Aestuariimicrobium kwangyangense

full scientific name: Aestuariimicrobium kwangyangense Jung et al. 2007

strain designation: R27

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32073positive0.8-1.0 µm0.8-1.0 µmcoccus-shapedno
67771positive
69480positive100
120520positiveoval-shapedno

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_21549_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21549_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21549_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21549_4.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15788BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
37828MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
120520CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
15788positivegrowth28mesophilic
32073positivegrowth04-40
32073positiveoptimum30mesophilic
37828positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32073positivegrowth7.5-8.5alkaliphile
32073positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32073aerobe
67771aerobe
120520obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.603

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3207317057cellobiose+carbon source
3207328757fructose+carbon source
3207328260galactose+carbon source
3207317234glucose+carbon source
3207317716lactose+carbon source
3207317306maltose+carbon source
3207337684mannose+carbon source
3207328053melibiose+carbon source
3207316634raffinose+carbon source
3207326546rhamnose+carbon source
3207317814salicin+carbon source
3207330911sorbitol+carbon source
3207317992sucrose+carbon source
3207327082trehalose+carbon source
3207353424tween 20+carbon source
3207353423tween 40+carbon source
3207353425tween 60+carbon source
3207353426tween 80+carbon source
3207318222xylose+carbon source
320734853esculin+hydrolysis
3207317632nitrate+reduction
12052017632nitrate+reduction
12052016301nitrite-reduction

metabolite production

  • @ref: 120520
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32073acid phosphatase+3.1.3.2
32073alpha-galactosidase+3.2.1.22
32073catalase+1.11.1.6
120520oxidase-
120520catalase+1.11.1.6
120520urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120520--++-+--+-+-+++++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15788oil-contaminated tidal flat sedimentKwangyangRepublic of KoreaKORAsia
67770Oil-contaminated tidal flat sedimentKwangyangRepublic of KoreaKORAsia
67771From enrichment with degradation activity of diesel oilRepublic of KoreaKORAsia
120520Environment, Oil-contaminated tidal flat sedimentKwangyangRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_2514.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_72;96_1356;97_1610;98_1956;99_2514&stattab=map
  • Last taxonomy: Aestuariimicrobium kwangyangense subclade
  • 16S sequence: DQ830982
  • Sequence Identity:
  • Total samples: 2434
  • soil counts: 600
  • aquatic counts: 703
  • animal counts: 987
  • plant counts: 144

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
157881Risk group (German classification)
1205201Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15788
  • description: Aestuariimicrobium kwangyangense strain R27 16S ribosomal RNA gene, partial sequence
  • accession: DQ830982
  • length: 1472
  • database: ena
  • NCBI tax ID: 396389

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aestuariimicrobium kwangyangense DSM 215491120954.3wgspatric1120954
66792Aestuariimicrobium kwangyangense DSM 215492523533600draftimg1120954
67770Aestuariimicrobium kwangyangense DSM 21549GCA_000421525contigncbi1120954

GC content

@refGC-contentmethod
1578868.8
3207368.8-69.2
6777068.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.037yes
flagellatedno98.284yes
gram-positiveyes91.173yes
anaerobicno97.619yes
aerobicyes83.262yes
halophileno95.987no
spore-formingno92.517no
thermophileno97.781yes
glucose-utilyes85.716no
glucose-fermentno65.921no

External links

@ref: 15788

culture collection no.: DSM 21549, JCM 14204, KCTC 19182, CIP 109737

straininfo link

  • @ref: 81882
  • straininfo: 309523

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17766882Aestuariimicrobium kwangyangense gen. nov., sp. nov., an LL-diaminopimelic acid-containing bacterium isolated from tidal flat sediment.Jung SY, Kim HS, Song JJ, Lee SG, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.64917-02007Bacterial Typing Techniques, Base Composition, Catalase/biosynthesis, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Gasoline, Genes, rRNA, Geologic Sediments/*microbiology, Hydrocarbons/metabolism, Korea, Molecular Sequence Data, Peptidoglycan/chemistry, Phylogeny, Propionibacteriaceae/chemistry/*classification/genetics/*isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysisGenetics
Phylogeny30141771Aestuariimicrobium soli sp. nov., isolated from farmland soil, and emended description of the genus Aestuariimicrobium.Chen LL, Chen F, Zhao HZ, Feng ZZ, Zhang H, Huang XInt J Syst Evol Microbiol10.1099/ijsem.0.0029862018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, *Farms, Fatty Acids/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Propionibacteriaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15788Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21549)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21549
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
32073Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2832028776041
37828Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7513
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
81882Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309523.1StrainInfo: A central database for resolving microbial strain identifiers
120520Curators of the CIPCollection of Institut Pasteur (CIP 109737)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109737