Strain identifier

BacDive ID: 7281

Type strain: Yes

Species: Agromyces atrinae

Strain Designation: P27

Strain history: <- JW Bae, KRIBB

NCBI tax ID(s): 592376 (species)

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

@ref: 17418

BacDive-ID: 7281

DSM-Number: 23870

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

description: Agromyces atrinae P27 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from traditional fermented seafood.

NCBI tax id

  • NCBI tax id: 592376
  • Matching level: species

strain history

@refhistory
17418<- JCM <- J.-W. Bae, Kyung Hee Univ., Seoul, Republic of Korea; P27 <- KCTC
67770J.-W. Bae P27.
67771<- JW Bae, KRIBB

doi: 10.13145/bacdive7281.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agromyces
  • species: Agromyces atrinae
  • full scientific name: Agromyces atrinae Park et al. 2010

@ref: 17418

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces atrinae

full scientific name: Agromyces atrinae Park et al. 2010

strain designation: P27

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29397positive1.5 µm0.75 µmrod-shapedno
67771positive
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
21416Rape yellow (1021)10-14 daysISP 2
2141610-14 daysISP 3
21416Oyster white (1013)10-14 daysISP 4
2141610-14 daysISP 5
21416Rape yellow (1021)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
21416noISP 2
21416noISP 3
21416noISP 4
21416noISP 5
21416noISP 7
21416

pigmentation

  • @ref: 29397
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17418BACTO 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
21416ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21416ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
21416ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21416ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21416ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
17418positivegrowth28mesophilic
29397positivegrowth10-37
29397positiveoptimum30mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
29397positivegrowth06-10alkaliphile
29397positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29397aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no92
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
21416NaClpositivemaximum2.5 %
29397NaClpositivegrowth0-4 %
29397NaClpositiveoptimum2 %

observation

  • @ref: 67770
  • observation: quinones: MK-12, MK-11, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2141617234glucose+
2141622599arabinose+
2141617992sucrose+
2141618222xylose+
2141617268myo-inositol-
2141637684mannose-
2141628757fructose-
2141626546rhamnose-
2141616634raffinose+
2141662968cellulose-
2939730089acetate+carbon source
2939717057cellobiose+carbon source
2939723652dextrin+carbon source
2939728757fructose+carbon source
2939728260galactose+carbon source
2939724265gluconate+carbon source
2939717234glucose+carbon source
2939717754glycerol+carbon source
2939728087glycogen+carbon source
2939717596inosine+carbon source
2939717716lactose+carbon source
2939717306maltose+carbon source
2939729864mannitol+carbon source
2939737684mannose+carbon source
2939715361pyruvate+carbon source
2939751850methyl pyruvate+carbon source
2939733942ribose+carbon source
2939717814salicin+carbon source
2939717992sucrose+carbon source
2939717748thymidine+carbon source
2939727082trehalose+carbon source
2939753423tween 40+carbon source
2939753426tween 80+carbon source
2939716704uridine+carbon source
2939718222xylose+carbon source
2939717632nitrate+reduction
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen+fermentation

enzymes

@refvalueactivityec
29397acid phosphatase+3.1.3.2
29397alpha-galactosidase+3.2.1.22
29397catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21416---+/--++-+-+------++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21416+++-++/-+/---+/-+-+-++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
17418traditional fermented seafoodRepublic of KoreaKORAsia
67770Traditional fermented seafoodRepublic of KoreaKORAsia
67771From Jeotgal, fermented shellfisgRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Seafood
#Engineered#Food production#Fermented

taxonmaps

  • @ref: 69479
  • File name: preview.99_63152.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_852;97_34675;98_44713;99_63152&stattab=map
  • Last taxonomy: Agromyces atrinae subclade
  • 16S sequence: FJ607310
  • Sequence Identity:
  • Total samples: 907
  • soil counts: 315
  • aquatic counts: 136
  • animal counts: 246
  • plant counts: 210

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
174181Risk group (German classification)
21416L1German classification

Sequence information

16S sequences

  • @ref: 17418
  • description: Agromyces atrinae strain P27 16S ribosomal RNA gene, partial sequence
  • accession: FJ607310
  • length: 1477
  • database: ena
  • NCBI tax ID: 592376

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces atrinae strain DSM 23870592376.3wgspatric592376
66792Agromyces atrinae strain DSM 23870592376.5wgspatric592376
66792Agromyces atrinae DSM 238702844837950draftimg592376
67770Agromyces atrinae DSM 23870GCA_013407835contigncbi592376
67770Agromyces atrinae DSM 23870GCA_004134805scaffoldncbi592376

GC content

@refGC-contentmethod
1741869.0thermal denaturation, midpoint method (Tm)
2939769
6777069thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
gram-positiveyes92.576no
anaerobicno99.603no
halophileno89.922no
spore-formingno90.526no
glucose-utilyes86.419no
thermophileno99.613yes
flagellatedno98.054yes
aerobicyes91.98yes
motileno91.156yes
glucose-fermentno86.992yes

External links

@ref: 17418

culture collection no.: DSM 23870, JCM 15913, KCTC 19593

straininfo link

  • @ref: 76732
  • straininfo: 399040

literature

  • topic: Phylogeny
  • Pubmed-ID: 19666805
  • title: Agromyces atrinae sp. nov., isolated from fermented seafood.
  • authors: Park EJ, Kim MS, Jung MJ, Roh SW, Chang HW, Shin KS, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.012294-0
  • year: 2009
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fermentation, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seafood/*microbiology, Sequence Analysis, DNA, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17418Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23870)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23870
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
21416Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM23870.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29397Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2580428776041
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
68379Automatically annotated from API Coryne
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
76732Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399040.1StrainInfo: A central database for resolving microbial strain identifiers