Strain identifier
BacDive ID: 23114
Type strain:
Species: Actinoplanes atraurantiacus
Strain Designation: Y16
Strain history: J. Zhang Y16.
NCBI tax ID(s): 1036182 (species)
General
@ref: 19176
BacDive-ID: 23114
DSM-Number: 45850
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Actinoplanes atraurantiacus Y16 is an aerobe, spore-forming, mesophilic bacterium that was isolated from forest soil.
NCBI tax id
- NCBI tax id: 1036182
- Matching level: species
strain history
@ref | history |
---|---|
19176 | <- JCM; JCM 17700 <- J. Zhang; Y16 |
67770 | J. Zhang Y16. |
doi: 10.13145/bacdive23114.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micromonosporales
- family: Micromonosporaceae
- genus: Actinoplanes
- species: Actinoplanes atraurantiacus
- full scientific name: Actinoplanes atraurantiacus Zhang et al. 2012
@ref: 19176
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micromonosporaceae
genus: Actinoplanes
species: Actinoplanes atraurantiacus
full scientific name: Actinoplanes atraurantiacus Zhang et al. 2012
strain designation: Y16
type strain: yes
Morphology
cell morphology
- @ref: 30488
- gram stain: positive
colony morphology
@ref | colony color | medium used |
---|---|---|
69446 | Golden yellow (1004) | ISP 5 |
69446 | Dahlia yellow (1033) | ISP 3 |
69446 | Daffodil yellow (1007) | ISP 4 |
69446 | Brown beige (1011) | ISP 7 |
69446 | Beige brown (8024) | suter with tyrosine |
69446 | Maize yellow (1006) | suter without tyrosine |
69446 | Pastel yellow (1034) | ISP 6 |
69446 | Yellow orange (2000) | ISP 2 |
multicellular morphology
@ref | forms multicellular complex | complex name | medium name |
---|---|---|---|
69446 | no | Aerial mycelium | ISP 2 |
69446 | no | Aerial mycelium | ISP 3 |
69446 | no | Aerial mycelium | ISP 4 |
69446 | no | Aerial mycelium | ISP 5 |
69446 | no | Aerial mycelium | ISP 6 |
69446 | no | Aerial mycelium | ISP 7 |
69446 | no | Aerial mycelium | suter with tyrosine |
69446 | no | Aerial mycelium | suter without tyrosine |
pigmentation
@ref | production | color | name |
---|---|---|---|
30488 | yes | ||
69446 | yes | Beige brown (8024), clay brown (8003) | soluble pigment |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
69446 | DSM_45850_image3.jpeg | Plates (553, ISP2, ISP3, ISP4, ISP5, ISP7) | Helmholtz-Zentrum für Infektionsforschung GmbH |
69446 | DSM_45850_image4.jpeg | Plates (553, ISP2, ISP3, ISP4, ISP5, ISP7) | Helmholtz-Zentrum für Infektionsforschung GmbH |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
19176 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf | |
19176 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf | |
19176 | GPHF-MEDIUM (DSMZ Medium 553) | yes | https://mediadive.dsmz.de/medium/553 | Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19176 | positive | growth | 28 | mesophilic |
30488 | positive | growth | 25-30 | mesophilic |
30488 | positive | optimum | 27.5 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
- @ref: 30488
- ability: positive
- type: growth
- pH: 06-09
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
- @ref: 30488
- oxygen tolerance: aerobe
spore formation
- @ref: 30488
- spore formation: yes
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30488 | NaCl | positive | growth | <3 % |
69446 | NaCl | positive | growth | 0 % |
observation
- @ref: 67770
- observation: quinones: MK-9(H4), MK-9(H2)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30488 | 17057 | cellobiose | + | carbon source |
30488 | 28260 | galactose | + | carbon source |
30488 | 17234 | glucose | + | carbon source |
30488 | 28087 | glycogen | + | carbon source |
30488 | 17716 | lactose | + | carbon source |
30488 | 17306 | maltose | + | carbon source |
30488 | 29864 | mannitol | + | carbon source |
30488 | 37684 | mannose | + | carbon source |
30488 | 26546 | rhamnose | + | carbon source |
30488 | 17814 | salicin | + | carbon source |
30488 | 17992 | sucrose | + | carbon source |
30488 | 18222 | xylose | + | carbon source |
30488 | 17632 | nitrate | + | reduction |
69446 | 22599 | arabinose | + | growth |
69446 | 62968 | cellulose | - | growth |
69446 | 28757 | fructose | + | growth |
69446 | 17234 | glucose | + | growth |
69446 | 17268 | inositol | + | growth |
69446 | 37684 | mannose | +/- | growth |
69446 | 16634 | raffinose | +/- | growth |
69446 | 26546 | rhamnose | +/- | growth |
69446 | 17992 | sucrose | + | growth |
69446 | 18222 | xylose | + | growth |
68379 | 17632 | nitrate | - | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 5291 | gelatin | + | hydrolysis |
68379 | 17634 | D-glucose | + | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30488 | acid phosphatase | + | 3.1.3.2 |
30488 | alkaline phosphatase | + | 3.1.3.1 |
30488 | gelatinase | + | |
30488 | urease | + | 3.5.1.5 |
68379 | gelatinase | + | |
68379 | beta-glucosidase | + | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68379 | alpha-glucosidase | - | 3.2.1.20 |
68379 | beta-galactosidase | + | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69446 | - | - | - | + | - | + | - | + | + | +/- | + | + | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69446 | + | +/- | +/- | - | + | +/- | - | +/- | + | + | + | +/- | + | - | +/- | + | + | +/- | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
19176 | forest soil | Yunnan Province | China | CHN | Asia |
67770 | Forest soil | Yunnan Province | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Forest |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_57520.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_1769;98_40991;99_57520&stattab=map
- Last taxonomy: Actinoplanes
- 16S sequence: HQ839788
- Sequence Identity:
- Total samples: 46
- soil counts: 33
- aquatic counts: 4
- animal counts: 3
- plant counts: 6
Safety information
risk assessment
- @ref: 19176
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19176
- description: Actinoplanes atraurantiacus strain Y16 16S ribosomal RNA gene, partial sequence
- accession: HQ839788
- length: 1402
- database: ena
- NCBI tax ID: 1036182
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Actinoplanes atraurantiacus strain CGMCC 4.6857 | 1036182.3 | wgs | patric | 1036182 |
66792 | Actinoplanes atraurantiacus CGMCC 4.6857 | 2675903134 | draft | img | 1036182 |
67770 | Actinoplanes atraurantiacus CGMCC 4.6857 | GCA_900215205 | scaffold | ncbi | 1036182 |
GC content
@ref | GC-content | method |
---|---|---|
19176 | 70.8 | thermal denaturation, midpoint method (Tm) |
30488 | 70.8 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 63.913 | no |
flagellated | no | 88.575 | no |
gram-positive | yes | 87.755 | yes |
anaerobic | no | 98.831 | yes |
aerobic | yes | 90.892 | yes |
halophile | no | 94.431 | yes |
spore-forming | yes | 91.782 | yes |
thermophile | no | 99.502 | yes |
glucose-util | yes | 90.665 | yes |
glucose-ferment | no | 88.276 | no |
External links
@ref: 19176
culture collection no.: DSM 45850, CGMCC 4.6857, JCM 17700
straininfo link
- @ref: 87351
- straininfo: 397613
literature
- topic: Phylogeny
- Pubmed-ID: 22180611
- title: Actinoplanes atraurantiacus sp. nov., isolated from soil.
- authors: Zhang Y, Zhang J, Fan L, Pang H, Xin Y, Zhang X
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.037226-0
- year: 2011
- mesh: Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Micromonosporaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, Sequence Analysis, DNA, Soil/analysis, *Soil Microbiology, Vitamin K 2/analysis
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
19176 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45850) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45850 | ||||
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 | ||||
30488 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26821 | 28776041 | ||
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) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68379 | Automatically annotated from API Coryne | ||||||
68382 | Automatically annotated from API zym | ||||||
69446 | Wink, J. | https://cdn.dsmz.de/wink/DSM%2045850.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | ||||
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 | ||||
87351 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397613.1 | StrainInfo: A central database for resolving microbial strain identifiers |