Strain identifier

BacDive ID: 132534

Type strain: Yes

Species: Agromyces binzhouensis

Strain Designation: OAct-353, OAct353

Strain history: CGMCC 4.7180 <-- J. Li; Ocean Univ. of China, China; OAct353.

NCBI tax ID(s): 1817495 (species)

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General

@ref: 24323

BacDive-ID: 132534

DSM-Number: 28305

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

description: Agromyces binzhouensis OAct-353 is an aerobe, heterotroph, Gram-positive bacterium that forms circular colonies and was isolated from soil from a coastal wetland river delta.

NCBI tax id

  • NCBI tax id: 1817495
  • Matching level: species

strain history

@refhistory
24323<- J. Li, Ocean Univ. China, Qingdao, P. R. China; OAct-353 <- G. Feng
67770CGMCC 4.7180 <-- J. Li; Ocean Univ. of China, China; OAct353.

doi: 10.13145/bacdive132534.20230509.8.1

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 binzhouensis
  • full scientific name: Agromyces binzhouensis Chen et al. 2016

@ref: 24323

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces binzhouensis

full scientific name: Agromyces binzhouensis Chen et al. 2016

strain designation: OAct-353, OAct353

type strain: yes

Morphology

cell morphology

  • @ref: 43631
  • gram stain: positive
  • cell length: 0.4-2 µm
  • cell width: 0.2-0.7 µm
  • cell shape: rod-shaped

colony morphology

  • @ref: 43631
  • colony size: 0.5-1 mm
  • colony color: Yellow
  • colony shape: circular
  • incubation period: 4 days
  • medium used: Yeast extract-malt extract agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43631Yeast extract-malt extract agaryes
24323TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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
43631positivegrowth12-36
43631positiveoptimum28mesophilic
24323positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
43631positivegrowth5-8
43631positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43631
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 43631
  • type: heterotroph

spore formation

  • @ref: 43631
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43631NaClpositivegrowth0-10 %(w/v)
43631NaClpositiveoptimum2-3 %(w/v)

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43631casein-hydrolysis
43631esculin-hydrolysis4853
43631gelatin-hydrolysis5291
43631starch-hydrolysis28017
43631urea-hydrolysis16199
43631nitrate-reduction17632
43631arbutin+oxidation18305
43631D-mannitol+oxidation16899
43631D-psicose+oxidation27605
43631raffinose+oxidation16634
43631D-ribose+oxidation16988
43631D-xylose+oxidation65327
43631glycerol+oxidation17754
43631L-alaninamide+oxidation21217
43631L-arabinose+oxidation30849
43631methyl beta-D-galactoside+oxidation17540
43631pyruvate+oxidation15361
43631salicin+oxidation17814
43631sucrose+oxidation17992
43631thymidine+oxidation17748
43631thymidine 5'-monophosphate+oxidation63528
43631tween 40+oxidation53423
43631tween 80+oxidation53426

metabolite production

@refChebi-IDmetaboliteproduction
4363116136hydrogen sulfideno
4363135581indoleyes

enzymes

@refvalueactivityec
43631pyrazinamidase+3.5.1.B15
43631leucine arylamidase+3.4.11.1
43631valine arylamidase+
43631acid phosphatase+3.1.3.2
43631alpha-chymotrypsin+3.4.21.1
43631esterase Lipase (C 8)+
43631cystine arylamidase+3.4.11.3
43631esterase (C 4)+
43631beta-galactosidase+3.2.1.23
43631beta-glucosidase-3.2.1.21
43631phosphohydrolase-
43631N-acetyl-beta-glucosaminidase-3.2.1.52
43631alkaline phosphatase-3.1.3.1
43631pyrrolidonyl arylamidase-3.4.19.3
43631trypsin-3.4.21.4
43631alpha-fucosidase-3.2.1.51
43631alpha-galactosidase-3.2.1.22
43631alpha-glucosidase-3.2.1.20
43631beta-glucuronidase-3.2.1.31
43631lipase (C 14)-
43631urease-3.5.1.5
43631alpha-mannosidase-3.2.1.24
43631cytochrome oxidase-1.9.3.1
43631catalase-1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
24323soil from a coastal wetland river deltaShandong, Binzhou, Yellow River deltaChinaCHNAsia
43631a soil sample collected from a coastal wetland of the Yellow River deltaBinzhou, ShandongChinaCHNAsia
67770Soil from a coastal wetland of the Yellow River delta in BinzhouShandongChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#River (Creek)
#Environmental#Terrestrial#Coast
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Wetland (Swamp)

Safety information

risk assessment

  • @ref: 24323
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24323
  • description: Agromyces binzhouensis strain OAct353 16S ribosomal RNA gene, partial sequence
  • accession: KC493987
  • length: 1451
  • database: ena
  • NCBI tax ID: 1817495

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces binzhouensis strain CGMCC 4.71801817495.5wgspatric1817495
66792Agromyces binzhouensis CGMCC 4.71802866589525draftimg1817495
67770Agromyces binzhouensis CGMCC 4.7180GCA_004135055contigncbi1817495

GC content

  • @ref: 24323
  • GC-content: 69.6
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno89.582no
gram-positiveyes92.595no
anaerobicno99.611yes
aerobicyes94.826no
halophileno84.393no
spore-formingno93.82yes
glucose-utilyes88.061no
flagellatedno97.519no
thermophileno99.177no
glucose-fermentno90.698no

External links

@ref: 24323

culture collection no.: DSM 28305, CGMCC 4.7180, NRRL B-59115, JCM 32487

straininfo link

  • @ref: 90860
  • straininfo: 404915

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26977901Agromyces binzhouensis sp. nov., an actinobacterium isolated from a coastal wetland of the Yellow River Delta.Chen Z, Guan Y, Wang J, Li JInt J Syst Evol Microbiol10.1099/ijsem.0.0010222016Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry, *WetlandsTranscriptome
Phylogeny33913805Protaetiibacter larvae sp. nov. and Agromyces intestinalis sp. nov., isolated from the gut of larvae of Protaetia brevitarsis seulensis, reclassification of Lysinimonas yzui as Pseudolysinimonas yzui comb. nov. and emended description of the genus Pseudolysinimonas.Lee SA, Heo J, Kim MA, Tamura T, Saitou S, Kwon SW, Weon HYInt J Syst Evol Microbiol10.1099/ijsem.0.0046692021Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Coleoptera/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Glycolipids/chemistry, Larva/microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

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
24323Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28305Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28305)
43631Zhirong Chen, Yingying Guan, Jingjing Wang and Jing LiAgromyces binzhouensis sp. nov., an actinobacterium isolated from a coastal wetland of the Yellow River Delta10.1099/ijsem.0.001022IJSEM 66: 2278-2283 201626977901
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
90860Reimer, 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-ID404915.1