Strain identifier

BacDive ID: 16911

Type strain: Yes

Species: Actinocorallia herbida

Strain history: IFO 15485 <-- Takeda Chem. Ind., Ltd.; AL-50780.

NCBI tax ID(s): 58109 (species)

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General

@ref: 11626

BacDive-ID: 16911

DSM-Number: 44254

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic

description: Actinocorallia herbida DSM 44254 is a spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 58109
  • Matching level: species

strain history

@refhistory
11626<- IFO <- S. Iinuma, Takeda Chem. Ind., AL-50780
67770IFO 15485 <-- Takeda Chem. Ind., Ltd.; AL-50780.

doi: 10.13145/bacdive16911.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Actinocorallia
  • species: Actinocorallia herbida
  • full scientific name: Actinocorallia herbida Iinuma et al. 1994

@ref: 11626

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinocorallia

species: Actinocorallia herbida

full scientific name: Actinocorallia herbida Iinuma et al. 1994

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.592
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11626GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
11626CORYNEBACTERIUM AGAR (DSMZ Medium 53)yeshttps://mediadive.dsmz.de/medium/53Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
11626positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

  • @ref: 11626
  • compound: azaserine-like antibiotic

observation

@refobservation
67770Production of Azaserine-like antibiotic
67770quinones: MK-9(H4), MK-9(H6)

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11626soilBangkokThailandTHAAsia
67770SoilBangkokThailandTHAAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_18416.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_9402;97_11308;98_13907;99_18416&stattab=map
  • Last taxonomy: Actinocorallia herbida
  • 16S sequence: LC066303
  • Sequence Identity:
  • Total samples: 241
  • soil counts: 21
  • aquatic counts: 1
  • animal counts: 3
  • plant counts: 216

Safety information

risk assessment

  • @ref: 11626
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinocorallia herbida 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAF134109403ena58109
20218Actinocorallia herbida gene for 16S ribosomal RNA, partial sequenceD854731465ena58109
67770Actinocorallia herbida gene for 16S ribosomal RNA, partial sequence, strain: JCM 9647LC0663031452ena58109

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinocorallia herbida strain DSM 4425458109.3wgspatric58109
66792Actinocorallia herbida DSM 442542784132147draftimg58109
67770Actinocorallia herbida DSM 44254GCA_003751225contigncbi58109

GC content

  • @ref: 11626
  • GC-content: 73
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes87.326no
anaerobicno98.416no
halophileno88.674no
spore-formingyes91.761no
glucose-utilyes87.83no
thermophileno98.709yes
flagellatedno98.135no
aerobicyes86.647no
motileno93.941no
glucose-fermentno92.496no

External links

@ref: 11626

culture collection no.: DSM 44254, ATCC 51528, IFO 15485, JCM 9647, NBRC 15485, NCIMB 13337, VKM Ac-1994, IMSNU 21271

straininfo link

  • @ref: 85916
  • straininfo: 93001

literature

  • topic: Phylogeny
  • Pubmed-ID: 12139476
  • title: Cell wall teichoic acids of actinomycetes of three genera of the order actinomycetales.
  • authors: Streshinskaya GM, Shashkov AS, Usov AI, Evtushenko LI, Naumova IB
  • journal: Biochemistry (Mosc)
  • DOI: 10.1023/a:1016348724308
  • year: 2002
  • mesh: Actinomycetales/*chemistry/*classification, Cell Wall/*chemistry, Magnetic Resonance Spectroscopy, Teichoic Acids/*analysis

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11626Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44254)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44254
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
85916Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID93001.1StrainInfo: A central database for resolving microbial strain identifiers