Strain identifier
BacDive ID: 17006
Type strain:
Species: Actinoallomurus spadix
Strain Designation: FYU A 116, A-116
Strain history: CIP <- 1998, JCM <- KCC: strain A-0146 <- H. Nonomura: strain A-116
NCBI tax ID(s): 79912 (species)
General
@ref: 11035
BacDive-ID: 17006
DSM-Number: 43459
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive
description: Actinoallomurus spadix FYU A 116 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 79912
- Matching level: species
strain history
@ref | history |
---|---|
11035 | <- M. Goodfellow <- KCC <- H. Nonomura, FYU, A 116 |
67770 | KCC A-0146 <-- H. Nonomura A-116. |
67771 | <- NCIMB <- H Nonomura A-116 |
122686 | CIP <- 1998, JCM <- KCC: strain A-0146 <- H. Nonomura: strain A-116 |
doi: 10.13145/bacdive17006.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Thermomonosporaceae
- genus: Actinoallomurus
- species: Actinoallomurus spadix
- full scientific name: Actinoallomurus spadix (Nonomura and Ohara 1971) Tamura et al. 2009
synonyms
- @ref: 20215
- synonym: Actinomadura spadix
@ref: 11035
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Thermomonosporaceae
genus: Actinoallomurus
species: Actinoallomurus spadix
full scientific name: Actinoallomurus spadix (Nonomura and Ohara 1971) Tamura et al. 2009
strain designation: FYU A 116, A-116
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility |
---|---|---|---|
67771 | positive | ||
122686 | positive | rod-shaped | no |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
11035 | ISP2 MEDIUM (DSMZ Medium 987) | yes | https://mediadive.dsmz.de/medium/987 | Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water |
32726 | MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicum | yes | Distilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g) | |
11035 | 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 |
122686 | CIP Medium 194 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=194 | |
122686 | CIP Medium 116 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18494 | positive | optimum | 28 | mesophilic |
32726 | positive | growth | 37 | mesophilic |
11035 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
67771 | positive | growth | 37 | mesophilic |
122686 | positive | growth | 15-41 | |
122686 | no | growth | 5 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
18494 | NaCl | positive | maximum | 2.5 % |
122686 | NaCl | positive | growth | 0 % |
122686 | NaCl | no | growth | 2 % |
122686 | NaCl | no | growth | 4 % |
122686 | NaCl | no | growth | 6 % |
122686 | NaCl | no | growth | 8 % |
122686 | NaCl | no | growth | 10 % |
observation
@ref | observation |
---|---|
67770 | quinones: MK-9(H8), MK-9(H6), MK-9(H4) |
67771 | quinones: MK-9(H_8_), MK-9(H_6_), MK-9(H_4_) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
18494 | 17234 | glucose | + | |
18494 | 22599 | arabinose | +/- | |
18494 | 17992 | sucrose | +/- | |
18494 | 18222 | xylose | +/- | |
18494 | 17268 | myo-inositol | +/- | |
18494 | 29864 | mannitol | +/- | |
18494 | 28757 | fructose | +/- | |
18494 | 26546 | rhamnose | +/- | |
18494 | 16634 | raffinose | +/- | |
18494 | 62968 | cellulose | +/- | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68368 | 5291 | gelatin | + | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | - | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
122686 | 4853 | esculin | + | hydrolysis |
122686 | 17632 | nitrate | + | reduction |
122686 | 16301 | nitrite | - | reduction |
antibiotic resistance
- @ref: 122686
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: yes
- is resistant: no
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
122686 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test | methylred-test |
---|---|---|---|---|---|
68368 | 15688 | acetoin | + | ||
68368 | 35581 | indole | - | ||
122686 | 15688 | acetoin | - | ||
122686 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68368 | gelatinase | + | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | - | 3.2.1.23 |
122686 | oxidase | - | |
122686 | beta-galactosidase | - | 3.2.1.23 |
122686 | alcohol dehydrogenase | - | 1.1.1.1 |
122686 | gelatinase | - | |
122686 | amylase | - | |
122686 | caseinase | + | 3.4.21.50 |
122686 | catalase | + | 1.11.1.6 |
122686 | gamma-glutamyltransferase | - | 2.3.2.2 |
122686 | lysine decarboxylase | - | 4.1.1.18 |
122686 | ornithine decarboxylase | - | 4.1.1.17 |
122686 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
122686 | tryptophan deaminase | - | |
122686 | urease | - | 3.5.1.5 |
68382 | esterase (C 4) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18494 | + | - | + | - | + | - | + | + | - | + | + | + | + | - | + | - | + | - | - | |
122686 | - | - | - | - | + | - | - | - | - | + | + | - | - | - | + | - | + | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
18494 | - | - | - | - | - | - | - | - | - | + | + |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122686 | +/- | - | +/- | +/- | +/- | +/- | - | +/- | - | +/- | +/- | +/- | +/- | - | +/- | - | - | +/- | - | - | - | - | - | - | +/- | - | +/- | +/- | +/- | +/- | +/- | +/- | - | - | +/- | +/- | +/- | +/- | +/- | +/- | +/- | - | - | +/- | - | - | - | - | +/- |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | geographic location |
---|---|---|---|---|---|
11035 | soil | Japan | JPN | Asia | |
67770 | Soil, dry-heated | Japan | JPN | Asia | Yamanashi Pref. |
67771 | From soil , dry-heated | Japan | JPN | Asia | Yamanashi Pref. |
122686 | Environment, Soil | Japan | JPN | Asia | Yamanashi |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_67778.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_5383;97_6498;98_47763;99_67778&stattab=map
- Last taxonomy: Actinoallomurus spadix subclade
- 16S sequence: AJ293712
- Sequence Identity:
- Total samples: 426
- soil counts: 392
- aquatic counts: 6
- animal counts: 26
- plant counts: 2
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
18494 | 1 | German classification |
11035 | 1 | Risk group (German classification) |
122686 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Actinomadura spadix strain ATCC27298 16S ribosomal RNA gene, partial sequence | AF051380 | 118 | ena | 79912 |
20218 | Actinomadura spadix 16S ribosomal RNA gene, partial sequence | AF163120 | 1458 | ena | 79912 |
20218 | Actinomadura spadix 16S-23S ribosomal RNA intergenic spacer sequence | AF163131 | 395 | ena | 79912 |
11035 | Actinoallomurus spadix gene for 16S rRNA, partial sequence, strain: NBRC 14099 | AB364581 | 1449 | ena | 79912 |
67770 | Actinomadura spadix partial 16S rRNA gene, strain IMSNU 20015T | AJ293712 | 1488 | ena | 79912 |
Genome sequences
- @ref: 66792
- description: Actinoallomurus spadix KCTC 9252
- accession: GCA_024055725
- assembly level: contig
- database: ncbi
- NCBI tax ID: 79912
GC content
@ref | GC-content | method |
---|---|---|
11035 | 74 | |
67771 | 66.4 | thermal denaturation, midpoint method (Tm) |
67770 | 74 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 98.5 | no |
gram-positive | yes | 89.967 | yes |
anaerobic | no | 97.694 | yes |
aerobic | yes | 84.802 | yes |
halophile | no | 89.396 | no |
spore-forming | yes | 92.302 | no |
motile | no | 91.435 | no |
glucose-ferment | no | 88.73 | no |
thermophile | no | 98.089 | yes |
glucose-util | yes | 87.576 | no |
External links
@ref: 11035
culture collection no.: DSM 43459, ATCC 27298, BCRC 13386, CBS 261.72, CIP 105479, IFO 14099, IMET 9752, JCM 3146, KCC A-0146, KCTC 9252, NBRC 14099, NCIB 11118, NRRL B-16128, IMSNU 20015, MTCC 2556, NCIMB 11118, CCRC 13386, BRCC 13386
straininfo link
- @ref: 86007
- straininfo: 389340
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19567582 | Transfer of Actinomadura spadix Nonomura and Ohara 1971 to Actinoallomurus spadix gen. nov., comb. nov., and description of Actinoallomurus amamiensis sp. nov., Actinoallomurus caesius sp. nov., Actinoallomurus coprocola sp. nov., Actinoallomurus fulvus sp. nov., Actinoallomurus iriomotensis sp. nov., Actinoallomurus luridus sp. nov., Actinoallomurus purpureus sp. nov. and Actinoallomurus yoronensis sp. nov. | Tamura T, Ishida Y, Nozawa Y, Otoguro M, Suzuki K | Int J Syst Evol Microbiol | 10.1099/ijs.0.006858-0 | 2009 | Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Amino Acids/analysis, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Japan, Molecular Sequence Data, Peptidoglycan/chemistry, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytology | Genetics |
Phylogeny | 23002049 | Actinoallomurus acanthiterrae sp. nov., an actinomycete isolated from rhizosphere soil of the mangrove plant Acanthus ilicifolius. | Tang YL, Lin HP, Xie QY, Li L, Peng F, Deng Z, Hong K | Int J Syst Evol Microbiol | 10.1099/ijs.0.043380-0 | 2012 | Acanthaceae/*microbiology, Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan, Phospholipids/analysis, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
11035 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43459) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-43459 | |||
18494 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM43459.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 | |
32726 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17503 | ||||
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/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68368 | Automatically annotated from API 20E | |||||
68371 | Automatically annotated from API 50CH acid | |||||
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 | |||
86007 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID389340.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122686 | Curators of the CIP | Collection of Institut Pasteur (CIP 105479) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105479 |