Strain identifier

BacDive ID: 16994

Type strain: Yes

Species: Actinomadura chibensis

Strain history: Y. Mikami IFM 10266 <-- Chiba Univ. Hosp., Japan.

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General

@ref: 12265

BacDive-ID: 16994

DSM-Number: 45038

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Actinomadura chibensis DSM 45038 is a mesophilic bacterium that was isolated from human.

NCBI tax id

NCBI tax idMatching level
392828species
1220554strain

strain history

@refhistory
12265<- Y. Mikami, IFM <- K. Yazawa
67770Y. Mikami IFM 10266 <-- Chiba Univ. Hosp., Japan.

doi: 10.13145/bacdive16994.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Actinomadura
  • species: Actinomadura chibensis
  • full scientific name: Actinomadura chibensis Hanafy et al. 2008

@ref: 12265

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura chibensis

full scientific name: Actinomadura chibensis Hanafy et al. 2008

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12265N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
12265GYM 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

culture temp

@refgrowthtypetemperaturerange
12265positivegrowth37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6), MK-9(H4), MK-9(H8)

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12265humanJapanJPNAsia
67770SputumJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Human

taxonmaps

  • @ref: 69479
  • File name: preview.99_8009.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_1053;97_4550;98_5839;99_8009&stattab=map
  • Last taxonomy: Actinomadura
  • 16S sequence: AB264086
  • Sequence Identity:
  • Total samples: 293
  • soil counts: 208
  • aquatic counts: 34
  • animal counts: 4
  • plant counts: 47

Safety information

risk assessment

  • @ref: 12265
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Actinomadura chibensis gene for 16S rRNA, partial sequence
  • accession: AB264086
  • length: 1466
  • database: ena
  • NCBI tax ID: 392828

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura chibensis NBRC 1061071220554.3wgspatric1220554
66792Actinomadura chibensis strain JCM 14158392828.3wgspatric392828
66792Actinomadura chibensis NBRC 1061072675903560draftimg1220554
67770Actinomadura chibensis NBRC 106107GCA_001552135contigncbi1220554
67770Actinomadura chibensis JCM 14158GCA_008085895contigncbi392828

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.842no
gram-positiveyes89.715no
anaerobicno98.069no
aerobicyes89.847no
halophileno93.347no
spore-formingyes91.561no
glucose-utilyes89.719no
flagellatedno98.452no
thermophileno92.256yes
glucose-fermentno88.844no

External links

@ref: 12265

culture collection no.: DSM 45038, IFM 10266, JCM 14158, NBRC 106107

straininfo link

  • @ref: 85996
  • straininfo: 297503

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25805630Actinomadura syzygii sp. nov., an endophytic actinomycete isolated from the roots of a jambolan plum tree (Syzygium cumini L. Skeels).Rachniyom H, Matsumoto A, Indananda C, Duangmal K, Takahashi Y, Thamchaipenet AInt J Syst Evol Microbiol10.1099/ijs.0.0002032015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Syzygium/*microbiology, Thailand, Trees/microbiology, Vitamin K 2/analogs & derivatives/chemistryEnzymology
Phylogeny32724099Actinomadura decatromicini sp. nov., isolated from mountain soil in Thailand.Songsumanus A, Kuncharoen N, Kudo T, Yuki M, Ohkuma M, Igarashi Y, Tanasupawat SJ Antibiot (Tokyo)10.1038/s41429-020-0353-y2020Actinomadura/*genetics/*isolation & purification/ultrastructure, Genome, Fungal, Phylogeny, *Soil Microbiology, ThailandGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12265Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45038)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45038
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)
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
85996Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297503.1StrainInfo: A central database for resolving microbial strain identifiers