Strain identifier
BacDive ID: 16574
Type strain:
Species: Planobispora longispora
Strain Designation: Pb-1075
Strain history: KCC A-0092 <-- J. E. Thiemann Pb 1075.
NCBI tax ID(s): 28887 (species)
General
@ref: 10711
BacDive-ID: 16574
DSM-Number: 43041
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive
description: Planobispora longispora Pb-1075 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil from the shore of Uramaco.
NCBI tax id
- NCBI tax id: 28887
- Matching level: species
strain history
@ref | history |
---|---|
10711 | <- KCC <- J.E. Thiemann, Pb-1075 |
67770 | KCC A-0092 <-- J. E. Thiemann Pb 1075. |
doi: 10.13145/bacdive16574.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Streptosporangiaceae
- genus: Planobispora
- species: Planobispora longispora
- full scientific name: Planobispora longispora Thiemann and Beretta 1968 (Approved Lists 1980)
@ref: 10711
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptosporangiaceae
genus: Planobispora
species: Planobispora longispora
full scientific name: Planobispora longispora Thiemann and Beretta 1968
strain designation: Pb-1075
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
colony morphology
@ref | colony color | medium used |
---|---|---|
69220 | Beige (1001) | suter with tyrosine |
69220 | Beige (1001) | suter without tyrosine |
69220 | Ivory (1014) | ISP 2 |
69220 | Ivory (1014) | ISP 6 |
69220 | Light ivory (1015) | ISP 3 |
69220 | Light ivory (1015) | ISP 4 |
69220 | Oyster white (1013) | ISP 5 |
69220 | Oyster white (1013) | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | complex name | medium name |
---|---|---|---|
69220 | no | Aerial mycelium | ISP 2 |
69220 | no | Aerial mycelium | ISP 3 |
69220 | no | Aerial mycelium | ISP 4 |
69220 | no | Aerial mycelium | ISP 5 |
69220 | no | Aerial mycelium | ISP 6 |
69220 | no | Aerial mycelium | ISP 7 |
69220 | no | Aerial mycelium | suter with tyrosine |
69220 | no | Aerial mycelium | suter without tyrosine |
pigmentation
@ref | production | name |
---|---|---|
69220 | no | Melanin |
69220 | no | soluble pigment |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
69220 | DSM_43041_image3.jpeg | Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7) | Helmholtz-Zentrum für Infektionsforschung GmbH |
69220 | DSM_43041_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 |
---|---|---|---|---|
10711 | 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 |
10711 | GYM+S MEDIUM (DSMZ Medium 214) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium214.pdf |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
10711 | positive | growth | 28 | mesophilic |
19931 | positive | optimum | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore description | spore formation | confidence |
---|---|---|---|
19931 | Formation of spore chains (only spore pairs), spore surface smooth | yes | |
69481 | yes | 100 | |
69480 | yes | 99.999 |
halophily
- @ref: 69220
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0 %
observation
- @ref: 67770
- observation: quinones: MK-9(III,VIII-H4), MK-9(H2), MK-9
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
69220 | 22599 | arabinose | +/- | growth |
69220 | 62968 | cellulose | - | growth |
69220 | 28757 | fructose | +/- | growth |
69220 | 17234 | glucose | + | growth |
69220 | 17268 | inositol | +/- | growth |
69220 | 37684 | mannose | +/- | growth |
69220 | 16634 | raffinose | - | growth |
69220 | 26546 | rhamnose | - | growth |
69220 | 17992 | sucrose | - | growth |
69220 | 18222 | xylose | +/- | growth |
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 |
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 |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | - |
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-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 |
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 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
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 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
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 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69220 | + | - | - | + | - | +/- | + | + | + | - | + | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69220 | + | +/- | +/- | + | + | + | +/- | +/- | + | + | + | - | + | - | + | + | + | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
19931 | + | - | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
10711 | soil from the shore of Uramaco | Venezuela | VEN | Middle and South America |
67770 | Soil | Venezuela | VEN | Middle and South America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Coast |
#Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
10711 | 1 | Risk group (German classification) |
19931 | 1 | German classification |
Sequence information
16S sequences
- @ref: 20218
- description: Planobispora longispora gene for 16S ribosomal RNA, partial sequence
- accession: D85494
- length: 1472
- database: ena
- NCBI tax ID: 28887
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Planobispora longispora NBRC 13918 | GCA_016863135 | contig | ncbi | 28887 |
66792 | Planobispora longispora strain NBRC 13918 | 28887.3 | wgs | patric | 28887 |
GC content
- @ref: 67770
- GC-content: 71
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | yes | 88.635 | no |
anaerobic | no | 98.741 | no |
halophile | no | 94.339 | yes |
spore-forming | yes | 93.917 | no |
glucose-util | yes | 88.882 | yes |
motile | yes | 61.544 | no |
flagellated | no | 90.201 | no |
aerobic | yes | 85.884 | no |
thermophile | no | 97.681 | yes |
glucose-ferment | no | 91.492 | yes |
External links
@ref: 10711
culture collection no.: DSM 43041, ATCC 23867, CBS 115.69, IAM 14288, IFO 13879, IFO 13918, JCM 3092, KCC A-0092, NBRC 13879, NBRC 13918, NCIMB 13269, VKM Ac-700, BCRC 13637, CGMCC 4.1206, IMSNU 20108, KCTC 9176, MTCC 1070
straininfo link
- @ref: 85601
- straininfo: 38275
literature
- topic: Phylogeny
- Pubmed-ID: 24408527
- title: Planobispora takensis sp. nov., isolated from soil.
- authors: Ngaemthao W, Suriyachadkun C, Chunhametha S, Niemhom N, Thawai C, Sanglier JJ
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.057968-0
- year: 2014
- mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Trees/microbiology, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
10711 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43041) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-43041 | |||
19931 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM43041.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 | |
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/ | ||||
68368 | Automatically annotated from API 20E | |||||
68379 | Automatically annotated from API Coryne | |||||
68382 | Automatically annotated from API zym | |||||
69220 | Wink, J. | https://cdn.dsmz.de/wink/DSM%2043041.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 | |||
85601 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID38275.1 | StrainInfo: A central database for resolving microbial strain identifiers |