Strain identifier
BacDive ID: 16994
Type strain:
Species: Actinomadura chibensis
Strain history: Y. Mikami IFM 10266 <-- Chiba Univ. Hosp., Japan.
NCBI tax ID(s): 1220554 (strain), 392828 (species)
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 id | Matching level |
---|---|
392828 | species |
1220554 | strain |
strain history
@ref | history |
---|---|
12265 | <- Y. Mikami, IFM <- K. Yazawa |
67770 | Y. 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
@ref | name | growth | link | composition |
---|---|---|---|---|
12265 | N-Z-AMINE-MEDIUM (DSMZ Medium 554) | yes | https://mediadive.dsmz.de/medium/554 | Name: 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 |
12265 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
12265 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: MK-9(H6), MK-9(H4), MK-9(H8)
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
12265 | human | Japan | JPN | Asia |
67770 | Sputum | Japan | JPN | Asia |
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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Actinomadura chibensis NBRC 106107 | 1220554.3 | wgs | patric | 1220554 |
66792 | Actinomadura chibensis strain JCM 14158 | 392828.3 | wgs | patric | 392828 |
66792 | Actinomadura chibensis NBRC 106107 | 2675903560 | draft | img | 1220554 |
67770 | Actinomadura chibensis NBRC 106107 | GCA_001552135 | contig | ncbi | 1220554 |
67770 | Actinomadura chibensis JCM 14158 | GCA_008085895 | contig | ncbi | 392828 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 92.842 | no |
gram-positive | yes | 89.715 | no |
anaerobic | no | 98.069 | no |
aerobic | yes | 89.847 | no |
halophile | no | 93.347 | no |
spore-forming | yes | 91.561 | no |
glucose-util | yes | 89.719 | no |
flagellated | no | 98.452 | no |
thermophile | no | 92.256 | yes |
glucose-ferment | no | 88.844 | no |
External links
@ref: 12265
culture collection no.: DSM 45038, IFM 10266, JCM 14158, NBRC 106107
straininfo link
- @ref: 85996
- straininfo: 297503
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 25805630 | Actinomadura 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 A | Int J Syst Evol Microbiol | 10.1099/ijs.0.000203 | 2015 | Actinomycetales/*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/chemistry | Enzymology |
Phylogeny | 32724099 | Actinomadura decatromicini sp. nov., isolated from mountain soil in Thailand. | Songsumanus A, Kuncharoen N, Kudo T, Yuki M, Ohkuma M, Igarashi Y, Tanasupawat S | J Antibiot (Tokyo) | 10.1038/s41429-020-0353-y | 2020 | Actinomadura/*genetics/*isolation & purification/ultrastructure, Genome, Fungal, Phylogeny, *Soil Microbiology, Thailand | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
12265 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45038) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45038 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69479 | João 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 | |||
85996 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297503.1 | StrainInfo: A central database for resolving microbial strain identifiers |