Strain identifier
BacDive ID: 8035
Type strain:
Species: Virgisporangium ochraceum
Strain Designation: Yu-655-43
Strain history: CIP <- 2001, IFO
NCBI tax ID(s): 65505 (species)
General
@ref: 11980
BacDive-ID: 8035
DSM-Number: 44793
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Virgisporangium ochraceum Yu-655-43 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil, vegetable field.
NCBI tax id
- NCBI tax id: 65505
- Matching level: species
strain history
@ref | history |
---|---|
11980 | <- NBRC <- IFO <- M. Hayokawa, Yamanashi Univ.; Yu-655-43 |
33096 | 2001, IFO |
67770 | T. Tamura YU 655-43 <-- M. Hayakawa YU 655-43. |
67771 | <- NBRC (IFO) |
121385 | CIP <- 2001, IFO |
doi: 10.13145/bacdive8035.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micromonosporales
- family: Micromonosporaceae
- genus: Virgisporangium
- species: Virgisporangium ochraceum
- full scientific name: Virgisporangium ochraceum corrig. Tamura et al. 2001
synonyms
- @ref: 20215
- synonym: Virgosporangium ochraceum
@ref: 11980
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micromonosporaceae
genus: Virgisporangium
species: Virgisporangium ochraceum
full scientific name: Virgisporangium ochraceum Tamura et al. 2001
strain designation: Yu-655-43
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
67771 | positive | |||
69480 | positive | 100 | ||
121385 | positive | rod-shaped | no |
colony morphology
@ref | colony color | medium used | hemolysis ability |
---|---|---|---|
69362 | Deep orange (2011) | ISP 4 | |
69362 | Deep orange (2011) | ISP 6 | |
69362 | Deep orange (2011) | ISP 2 | |
69362 | Deep orange (2011) | ISP 3 | |
69362 | Beige red (3012), nut brown (8011) | ISP 7 | |
69362 | Pastel yellow (1034) | ISP 5 | |
69362 | Pastel yellow (1034) | suter without tyrosine | |
69362 | Pastel yellow (1034), ochre brown (8001) | suter with tyrosine | |
121385 | 1 |
multicellular morphology
@ref | forms multicellular complex | complex name | medium name |
---|---|---|---|
69362 | no | Aerial mycelium | ISP 2 |
69362 | no | Aerial mycelium | ISP 3 |
69362 | no | Aerial mycelium | ISP 4 |
69362 | no | Aerial mycelium | ISP 5 |
69362 | no | Aerial mycelium | ISP 6 |
69362 | no | Aerial mycelium | ISP 7 |
69362 | no | Aerial mycelium | suter with tyrosine |
69362 | no | Aerial mycelium | suter without tyrosine |
pigmentation
@ref | production | name | color |
---|---|---|---|
69362 | yes | Melanin | |
69362 | yes | soluble pigment | Copper brown (8004), ochre brown (8001) |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
69362 | DSM_44793_image3.jpeg | Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7) | Helmholtz-Zentrum für Infektionsforschung GmbH |
69362 | DSM_44793_image4.jpeg | Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7) | Helmholtz-Zentrum für Infektionsforschung GmbH |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
11980 | STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) | yes | https://mediadive.dsmz.de/medium/252 | Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water |
11980 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://mediadive.dsmz.de/medium/84 | Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water |
33096 | MEDIUM 122 - for Streptomyces | yes | Distilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (2.000 g);Starch maize (10.000 g) | |
121385 | CIP Medium 366 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=366 | |
121385 | CIP Medium 122 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=122 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
11980 | positive | growth | 28 | mesophilic |
33096 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
121385 | positive | growth | 25-41 | |
121385 | no | growth | 10 | psychrophilic |
121385 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
67771 | aerobe |
121385 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 99.999 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
69362 | NaCl | positive | growth | 0 % |
121385 | NaCl | positive | growth | 0-2 % |
121385 | NaCl | no | growth | 4 % |
121385 | NaCl | no | growth | 6 % |
121385 | NaCl | no | growth | 8 % |
121385 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-10(H4), MK-10(H6), MK-10(H8)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
69362 | 22599 | arabinose | + | growth |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
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 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 28066 | gentiobiose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | + | builds acid from |
68371 | 17992 | sucrose | + | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | + | builds acid from |
68371 | 17057 | cellobiose | - | 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 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | - | builds acid from |
68371 | 15824 | D-fructose | + | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 12936 | D-galactose | - | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | - | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
69362 | 62968 | cellulose | - | growth |
69362 | 28757 | fructose | + | growth |
69362 | 17234 | glucose | + | growth |
69362 | 17268 | inositol | + | growth |
69362 | 37684 | mannose | + | growth |
69362 | 16634 | raffinose | + | growth |
69362 | 26546 | rhamnose | + | growth |
69362 | 17992 | sucrose | + | growth |
69362 | 18222 | xylose | + | growth |
121385 | 16947 | citrate | - | carbon source |
121385 | 4853 | esculin | + | hydrolysis |
121385 | 606565 | hippurate | - | hydrolysis |
121385 | 17632 | nitrate | + | reduction |
121385 | 16301 | nitrite | + | reduction |
121385 | 17632 | nitrate | + | respiration |
68379 | 17632 | nitrate | + | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 16199 | urea | - | 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 |
antibiotic resistance
- @ref: 121385
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 121385
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
121385 | 15688 | acetoin | + | |
121385 | 17234 | glucose | + |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68379 | gelatinase | + | |
68379 | urease | - | 3.5.1.5 |
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 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
121385 | oxidase | - | |
121385 | beta-galactosidase | - | 3.2.1.23 |
121385 | alcohol dehydrogenase | + | 1.1.1.1 |
121385 | gelatinase | +/- | |
121385 | amylase | + | |
121385 | DNase | + | |
121385 | caseinase | + | 3.4.21.50 |
121385 | catalase | + | 1.11.1.6 |
121385 | tween esterase | - | |
121385 | gamma-glutamyltransferase | - | 2.3.2.2 |
121385 | lecithinase | + | |
121385 | lipase | - | |
121385 | lysine decarboxylase | - | 4.1.1.18 |
121385 | ornithine decarboxylase | - | 4.1.1.17 |
121385 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
121385 | protease | - | |
121385 | tryptophan deaminase | - | |
121385 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
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 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69362 | + | - | - | + | +/- | + | + | + | + | - | + | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69362 | + | + | + | - | + | + | +/- | + | + | + | +/- | + | + | +/- | + | + | + | + | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121385 | - | - | - | - | +/- | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - | - | + | - | - | +/- | - | - | + | - | - | + | + | - | - | - | +/- | - | - | - | +/- | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
11980 | soil, vegetable field | Yamanashi prefecture | Japan | JPN | Asia |
67770 | Soil of vegetable field | Yamanashi Pref. | Japan | JPN | Asia |
67771 | From soil | Japan | JPN | Asia | |
121385 | Environment, Soil, vegetable field | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | #Field |
#Environmental | #Terrestrial | #Soil |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
11980 | 1 | Risk group (German classification) |
20119 | 1 | German classification |
121385 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 11980
- description: Virgosporangium ochraceum gene for 16S rRNA, partial sequence, strain:YU655-43
- accession: AB006167
- length: 1466
- database: ena
- NCBI tax ID: 65505
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Virgisporangium ochraceum NBRC 16418 | GCA_016863655 | contig | ncbi | 65505 |
66792 | Virgisporangium ochraceum strain NBRC 16418 | 65505.3 | wgs | patric | 65505 |
GC content
@ref | GC-content | method |
---|---|---|
11980 | 71 | |
67770 | 71 | high performance liquid chromatography (HPLC) |
67771 | 71.0 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | yes | 81.444 | yes |
anaerobic | no | 98.557 | yes |
halophile | no | 93.948 | yes |
spore-forming | yes | 79.682 | no |
glucose-util | yes | 87.098 | yes |
flagellated | no | 90.823 | no |
thermophile | no | 98.509 | no |
aerobic | yes | 87.598 | yes |
motile | yes | 59.701 | no |
glucose-ferment | no | 89.264 | yes |
External links
@ref: 11980
culture collection no.: DSM 44793, CCUG 46558, CIP 107213, IFO 16418, JCM 11001, KCTC 13915, NBRC 16418, BCRC 16330, CGMCC 4.5561, ATCC BAA-484
straininfo link
- @ref: 77465
- straininfo: 101059
literature
- topic: Phylogeny
- Pubmed-ID: 28698675
- title: Virgisporangium myanmarense sp. nov., a novel motile actinomycete isolated from an anthill soil in Myanmar.
- authors: Yamamura H, Miyazaki S, Ikoma K, Nakagawa Y, Hamada M, Otoguro M, Tamura T, Ando K, Phay N, Hayakawa M
- journal: J Antibiot (Tokyo)
- DOI: 10.1038/ja.2017.81
- year: 2017
- mesh: Aerobiosis, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Micromonosporaceae/*classification/genetics/*isolation & purification/physiology, Myanmar, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Soil Microbiology, Temperature, Vitamin K 2/analysis
- topic2: Transcriptome
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
11980 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44793) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44793 | |
20119 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44793.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 | |
33096 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/4624 | ||
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 | ||
68371 | Automatically annotated from API 50CH acid | |||
68379 | Automatically annotated from API Coryne | |||
68382 | Automatically annotated from API zym | |||
69362 | Wink, J. | https://cdn.dsmz.de/wink/DSM%2044793.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |
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 | |
77465 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID101059.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
121385 | Curators of the CIP | Collection of Institut Pasteur (CIP 107213) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107213 |