Strain identifier
BacDive ID: 132133
Type strain: 
Species: Amycolatopsis endophytica
Strain history: <- S Qin, Xuzhou Normal Univ., China
NCBI tax ID(s): 860233 (species)
version 8.1 (current version)
General
@ref: 23923
BacDive-ID: 132133
DSM-Number: 104006
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Amycolatopsis endophytica DSM 104006 is an aerobe, spore-forming, mesophilic bacterium that was isolated from healthy oil-seed plant Jatrophacurcas L.
NCBI tax id
- NCBI tax id: 860233
- Matching level: species
strain history
| @ref | history |
|---|---|
| 23923 | <- CCTCC; CCTCC AA2010003 |
| 67770 | KCTC 19776 <-- S. Qin; Xuzhou Normal Univ., China; KLBMP 1221. |
| 67771 | <- S Qin, Xuzhou Normal Univ., China |
doi: 10.13145/bacdive132133.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Amycolatopsis
- species: Amycolatopsis endophytica
- full scientific name: Amycolatopsis endophytica Miao et al. 2012
@ref: 23923
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Amycolatopsis
species: Amycolatopsis endophytica
full scientific name: Amycolatopsis endophytica Miao et al. 2012
type strain: yes
Morphology
cell morphology
| @ref | gram stain | motility | confidence |
|---|---|---|---|
| 67771 | positive | ||
| 69480 | no | 93.886 | |
| 69480 | positive | 100 |
multimedia
- @ref: 23923
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_104006.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 23923
- name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
- growth: yes
- link: https://mediadive.dsmz.de/medium/65
- composition: 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 |
|---|---|---|---|---|
| 23923 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
| 67771 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
observation
- @ref: 67770
- observation: quinones: MK-9(H4)
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 23923 | healthy oil-seed plant Jatrophacurcas L | Jatropha curcas | Sichuan Province, Panzhihua | China | CHN | Asia |
| 67770 | Surface-sterilized seeds of Jatropha curcas L. | Jatropha curcas | Panzhihua, Sichuan Province, south-west China | China | CHN | Asia |
| 67771 | From surface-sterilized seeds of an oil-seed plant `Jatropha curcas L.` | Sichuan Province | China | CHN | Asia |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Shrub (Scrub)
taxonmaps
- @ref: 69479
- File name: preview.99_129678.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_935;97_1087;98_1297;99_129678&stattab=map
- Last taxonomy: Amycolatopsis
- 16S sequence: HM153799
- Sequence Identity:
- Total samples: 5
- soil counts: 4
- animal counts: 1
Safety information
risk assessment
- @ref: 23923
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 23923
- description: Amycolatopsis endophytica strain KLBMP 1221 16S ribosomal RNA gene, partial sequence
- accession: HM153799
- length: 1443
- database: ena
- NCBI tax ID: 860233
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Amycolatopsis endophytica strain DSM 104006 | 860233.3 | wgs | patric | 860233 |
| 66792 | Amycolatopsis endophytica DSM 104006 | 2856431239 | draft | img | 860233 |
| 67770 | Amycolatopsis endophytica DSM 104006 | GCA_013410405 | contig | ncbi | 860233 |
GC content
- @ref: 23923
- GC-content: 73.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | no | 92.028 | no |
| flagellated | no | 97.48 | no |
| gram-positive | yes | 92.075 | yes |
| anaerobic | no | 99.283 | yes |
| halophile | no | 84.102 | no |
| spore-forming | yes | 88.61 | no |
| thermophile | no | 96.759 | no |
| glucose-util | yes | 90.993 | no |
| aerobic | yes | 94.256 | yes |
| glucose-ferment | no | 91.926 | no |
External links
@ref: 23923
culture collection no.: DSM 104006, CCTCC AA 2010003, JCM 31481, KCTC 19776, KLBMP 1221
straininfo link
- @ref: 90489
- straininfo: 408025
literature
- topic: Phylogeny
- Pubmed-ID: 21594685
- title: Amycolatopsis endophytica sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L.
- authors: Miao Q, Qin S, Bian GK, Yuan B, Xing K, Zhang YJ, Li Q, Tang SK, Li WJ, Jiang JH
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-011-9588-8
- year: 2011
- mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Endophytes/*classification/genetics/*isolation & purification/physiology, Jatropha/*microbiology, Molecular Sequence Data, Phylogeny, Seeds/microbiology
- topic2: Enzymology
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
| 23923 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-104006 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104006) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 90489 | Reimer, 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 identifiers | 10.60712/SI-ID408025.1 |