Strain identifier
BacDive ID: 13243
Type strain:
Species: Amycolatopsis rubida
Strain Designation: 13.4
Strain history: CIP <- 2001, JCM <- Z. Liu: strain 13.4
NCBI tax ID(s): 112413 (species)
General
@ref: 11946
BacDive-ID: 13243
DSM-Number: 44637
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic
description: Amycolatopsis rubida 13.4 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil of a conifer forest.
NCBI tax id
- NCBI tax id: 112413
- Matching level: species
strain history
@ref | history |
---|---|
11946 | <- T. Kudo, JCM <- Z. Liu; 13.4 |
67770 | Z. Liu 13.4. |
122282 | CIP <- 2001, JCM <- Z. Liu: strain 13.4 |
doi: 10.13145/bacdive13243.20230509.8.1
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 rubida
- full scientific name: Amycolatopsis rubida Huang et al. 2001
@ref: 11946
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Amycolatopsis
species: Amycolatopsis rubida
full scientific name: Amycolatopsis rubida Huang et al. 2001 emend. Nouioui et al. 2018
strain designation: 13.4
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 94.476 | ||
69480 | 100 | positive | ||
122282 | no | positive | filament-shaped |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
20084 | Beige (1001) | 10-14 days | ISP 2 |
20084 | Beige (1001) | 10-14 days | ISP 3 |
20084 | Beige (1001) | 10-14 days | ISP 4 |
20084 | Beige (1001) | 10-14 days | ISP 5 |
20084 | Beige (1001) | 10-14 days | ISP 6 |
20084 | Beige (1001) | 10-14 days | ISP 7 |
122282 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
20084 | no | ISP 2 |
20084 | no | ISP 3 |
20084 | no | ISP 4 |
20084 | no | ISP 5 |
20084 | no | ISP 6 |
20084 | no | ISP 7 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
11946 | 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 |
20084 | ISP 2 | yes | Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes | |
20084 | ISP 3 | yes | Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms: | |
20084 | ISP 4 | yes | Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml | |
20084 | ISP 5 | yes | Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes | |
20084 | ISP 6 | yes | Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes | |
20084 | ISP 7 | yes | Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes | |
39659 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
122282 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
11946 | positive | growth | 28 | mesophilic |
20084 | positive | optimum | 28 | mesophilic |
39659 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
122282 | positive | growth | 25-37 | mesophilic |
122282 | no | growth | 10 | psychrophilic |
122282 | no | growth | 41 | thermophilic |
122282 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 122282
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 99.62 |
halophily
- @ref: 122282
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-10 %
observation
- @ref: 67770
- observation: quinones: MK-9(H6)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
122282 | 16947 | citrate | - | carbon source |
122282 | 4853 | esculin | - | hydrolysis |
122282 | 606565 | hippurate | - | hydrolysis |
122282 | 17632 | nitrate | - | reduction |
122282 | 16301 | nitrite | - | reduction |
122282 | 17632 | nitrate | - | respiration |
antibiotic resistance
- @ref: 122282
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 122282
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
122282 | 15688 | acetoin | - | |
122282 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
122282 | oxidase | - | |
122282 | beta-galactosidase | - | 3.2.1.23 |
122282 | alcohol dehydrogenase | - | 1.1.1.1 |
122282 | gelatinase | + | |
122282 | amylase | - | |
122282 | DNase | - | |
122282 | caseinase | + | 3.4.21.50 |
122282 | catalase | + | 1.11.1.6 |
122282 | tween esterase | - | |
122282 | gamma-glutamyltransferase | + | 2.3.2.2 |
122282 | lecithinase | - | |
122282 | lipase | + | |
122282 | lysine decarboxylase | - | 4.1.1.18 |
122282 | ornithine decarboxylase | - | 4.1.1.17 |
122282 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
122282 | protease | + | |
122282 | tryptophan deaminase | - | |
122282 | urease | + | 3.5.1.5 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20084 | + | + | + | + | + | + | + | + | + | + | + | - | + | - | + | + | + | + | + | |
122282 | - | + | + | - | + | - | - | - | + | + | + | - | - | - | - | - | + | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122282 | + | + | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | - | + | - | - | + | - | + | - | - | - | - | + | + | + | - | - | - | + | - | + | + | - | - | - | - | - | - | - | + | + | + | - | - | + | + | - | + | - | - | + | + | + | + | - | - | + | - | - | - | - | - | + | + | + | + | + | - | - | - | + | + | - | - | - | - | - | + | - | + | + | + | + | + | + | + | - | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
11946 | soil of a conifer forest | Guangxi Province | China | CHN | Asia |
67770 | Soil of a conifer forest | Guangxi Province | China | CHN | Asia |
122282 | Environment, Soil, conifer forest | Guangxi | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Forest |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_7930.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_408;97_462;98_606;99_7930&stattab=map
- Last taxonomy: Amycolatopsis
- 16S sequence: AF222022
- Sequence Identity:
- Total samples: 101
- soil counts: 59
- animal counts: 14
- plant counts: 28
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
11946 | 1 | Risk group (German classification) |
20084 | 1 | German classification |
122282 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 20218
- description: Amycolatopsis rubidus 16S ribosomal RNA gene, partial sequence
- accession: AF222022
- length: 1402
- database: ena
- NCBI tax ID: 112413
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Amycolatopsis rubida strain DSM 44637 | 112413.4 | wgs | patric | 112413 |
66792 | Amycolatopsis rubida DSM 44637 | 2675903692 | draft | img | 112413 |
67770 | Amycolatopsis rubida DSM 44637 | GCA_900115345 | contig | ncbi | 112413 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 69.8 | genome sequence analysis |
67770 | 67.4 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 94.647 | no |
flagellated | no | 97.598 | no |
gram-positive | yes | 87.818 | no |
anaerobic | no | 99.099 | no |
aerobic | yes | 92.662 | no |
halophile | no | 89.611 | no |
spore-forming | yes | 93.727 | no |
thermophile | no | 94.922 | yes |
glucose-util | yes | 89.483 | no |
glucose-ferment | no | 91.966 | no |
External links
@ref: 11946
culture collection no.: DSM 44637, AS 4.1541, CIP 107102, JCM 10871, NRRL B-24150, ATCC BAA 726, CGMCC 4.1541, KCTC 19909, NBRC 100041
straininfo link
- @ref: 82448
- straininfo: 100502
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 11414266 | Amycolatopsis rubida sp. nov., a new Amycolatopsis species from soil. | Huang Y, Qi W, Lu Z, Liu Z, Goodfellow M | Int J Syst Evol Microbiol | 10.1099/00207713-51-3-1093 | 2001 | Actinomycetales/*classification/genetics/isolation & purification/ultrastructure, Carbohydrate Metabolism, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology | Genetics |
Phylogeny | 34287120 | Amycolatopsis dendrobii sp. nov., an endophytic actinomycete isolated from Dendrobium heterocarpum Lindl. | Tedsree N, Tanasupawat S, Sritularak B, Kuncharoen N, Likhitwitayawuid K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004902 | 2021 | Amycolatopsis/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Dendrobium/*microbiology, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hantavirus, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
11946 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44637) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44637 | |||
20084 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44637.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
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 | |
39659 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/19305 | ||||
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/ | ||||
68382 | Automatically annotated from API zym | |||||
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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
82448 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100502.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122282 | Curators of the CIP | Collection of Institut Pasteur (CIP 107102) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107102 |