Strain identifier
BacDive ID: 11509
Type strain:
Species: Paenibacillus curdlanolyticus
Strain Designation: Yk9
Strain history: CIP <- 1995, IFO <- 1995, T. Harada, Kobe Women's Univ., Japan: strain YK9
NCBI tax ID(s): 717606 (strain), 59840 (species)
General
@ref: 3867
BacDive-ID: 11509
DSM-Number: 10247
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped
description: Paenibacillus curdlanolyticus Yk9 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil.
NCBI tax id
NCBI tax id | Matching level |
---|---|
59840 | species |
717606 | strain |
strain history
@ref | history |
---|---|
3867 | <- IFO |
67770 | NBRC 15724 <-- IFO 15724 <-- T. Harada YK9. |
118820 | CIP <- 1995, IFO <- 1995, T. Harada, Kobe Women's Univ., Japan: strain YK9 |
doi: 10.13145/bacdive11509.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Paenibacillaceae
- genus: Paenibacillus
- species: Paenibacillus curdlanolyticus
- full scientific name: Paenibacillus curdlanolyticus (Kanzawa et al. 1995) Shida et al. 1997
synonyms
- @ref: 20215
- synonym: Bacillus curdlanolyticus
@ref: 3867
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus curdlanolyticus
full scientific name: Paenibacillus curdlanolyticus (Kanzawa et al. 1995) Shida et al. 1997
strain designation: Yk9
type strain: yes
Morphology
cell morphology
- @ref: 118820
- gram stain: positive
- cell shape: rod-shaped
- motility: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
3867 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535; with strain-specific modifications) Composition: Trypticase soy broth 30.0 g/l Distilled water |
3867 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
38509 | MEDIUM 11 - for Agromyces | yes | Distilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (5.000g);Yeast extract (3.000 g);Peptone (5.000 g);Di Potassium monohydrogenophosphate (0.200 g) | |
118820 | CIP Medium 11 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=11 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3867 | positive | growth | 30 | mesophilic |
38509 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
118820 | positive | growth | 30-37 | mesophilic |
118820 | no | growth | 10 | psychrophilic |
118820 | no | growth | 45 | thermophilic |
118820 | no | growth | 55 | thermophilic |
culture pH
- @ref: 118820
- ability: positive
- type: growth
- pH: 6
Physiology and metabolism
oxygen tolerance
- @ref: 118820
- oxygen tolerance: obligate aerobe
spore formation
- @ref: 118820
- spore formation: yes
compound production
- @ref: 3867
- compound: exo-(1-3)-ß-D glucanase
observation
- @ref: 67770
- observation: quinones: MK-7
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | + | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | + | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | lactose | - | builds acid from | 17716 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | + | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | - | builds acid from | 16024 |
68371 | D-fructose | - | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
118820 | citrate | - | carbon source | 16947 |
118820 | nitrate | + | reduction | 17632 |
118820 | nitrite | - | reduction | 16301 |
118820 | nitrate | - | respiration | 17632 |
metabolite production
- @ref: 118820
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 118820
- Chebi-ID: 15688
- metabolite: acetoin
- voges-proskauer-test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
118820 | oxidase | + | |
118820 | gelatinase | - | |
118820 | amylase | + | |
118820 | catalase | + | 1.11.1.6 |
118820 | 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 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
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 zym
@ref | Control | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118820 | - | + | + | + | - | - | - | - | - | - | - | + | - | - | - | + | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118820 | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | +/- | - | +/- | - | - | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | geographic location | isolation date |
---|---|---|---|---|---|---|
3867 | soil | Japan | JPN | Asia | ||
67770 | Soil | Japan | JPN | Asia | Kobe City | |
118820 | Environment, Soil | Japan | JPN | Asia | Kobe | 1990 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_4777.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_2361;97_2875;98_3580;99_4777&stattab=map
- Last taxonomy: Paenibacillus curdlanolyticus subclade
- 16S sequence: AB680947
- Sequence Identity:
- Total samples: 2460
- soil counts: 1279
- aquatic counts: 201
- animal counts: 756
- plant counts: 224
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
3867 | 1 | Risk group (German classification) |
118820 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Paenibacillus curdlanolyticus gene for 16S rRNA, partial sequence | AB073202 | 1531 | ena | 717606 |
20218 | Paenibacillus curdlanolyticus DNA for 16S rRNA | D78466 | 1436 | ena | 717606 |
20218 | Paenibacillus curdlanolyticus gene for 16S rRNA, partial sequence, strain: NBRC 15724 | AB680947 | 1478 | ena | 59840 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paenibacillus curdlanolyticus YK9 | 717606.6 | wgs | patric | 717606 |
66792 | Paenibacillus curdlanolyticus YK9 | 648276707 | draft | img | 717606 |
67770 | Paenibacillus curdlanolyticus YK9 | GCA_000179615 | scaffold | ncbi | 717606 |
GC content
@ref | GC-content | method |
---|---|---|
3867 | 51.6 | high performance liquid chromatography (HPLC) |
67770 | 51.5 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 85.987 | no |
flagellated | yes | 80.146 | no |
gram-positive | yes | 88.884 | no |
anaerobic | no | 99.031 | no |
aerobic | yes | 87.768 | no |
halophile | no | 97.812 | no |
spore-forming | yes | 96.784 | no |
thermophile | no | 98.709 | yes |
glucose-util | yes | 89.366 | no |
glucose-ferment | no | 89.536 | no |
External links
@ref: 3867
culture collection no.: DSM 10247, IFO 15724, NBRC 15724, JCM 12163, ATCC 51898, CCM 4536, CIP 104575, HSCC 491, KCTC 3759, LMG 18050, NRRL B-23243
straininfo link
- @ref: 80741
- straininfo: 10548
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 8590679 | Bacillus curdlanolyticus sp. nov. and Bacillus kobensis sp. nov., which hydrolyze resistant curdlan. | Kanzawa Y, Harada A, Takeuchi M, Yokota A, Harada T | Int J Syst Bacteriol | 10.1099/00207713-45-3-515 | 1995 | Aerobiosis, Bacillus/*classification/genetics/metabolism, Bacterial Proteins/chemistry, Base Composition, Carbohydrate Metabolism, Culture Media, DNA, Bacterial/chemistry/genetics, Electrophoresis, Polyacrylamide Gel, Fatty Acids/chemistry, Glucans/*metabolism, Nucleic Acid Hybridization, Polysaccharides, Bacterial/*metabolism, Sequence Homology, Nucleic Acid, *Soil Microbiology, Spores, *beta-Glucans | Metabolism |
Phylogeny | 12361272 | Paenibacillus glycanilyticus sp. nov., a novel species that degrades heteropolysaccharide produced by the cyanobacterium Nostoc commune. | Dasman, Kajiyama S, Kawasaki H, Yagi M, Seki T, Fukusaki E, Kobayashi A | Int J Syst Evol Microbiol | 10.1099/00207713-52-5-1669 | 2002 | Bacillus/*classification/genetics/isolation & purification/metabolism, Base Composition, Base Sequence, Biodegradation, Environmental, Cyanobacteria/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gram-Positive Endospore-Forming Rods/*classification/genetics/isolation & purification/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, Polysaccharides, Bacterial/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology | Metabolism |
Phylogeny | 25516431 | Paenibacillus ginsengiterrae sp. nov., a ginsenoside-hydrolyzing bacteria isolated from soil of ginseng field. | Huq MA, Kim YJ, Hoang VA, Siddiqi MZ, Yang DC | Arch Microbiol | 10.1007/s00203-014-1073-0 | 2014 | Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Ginsenosides/*metabolism, Lipids/analysis, Molecular Sequence Data, Oxidoreductases/metabolism, Paenibacillus/chemistry/*classification/genetics/isolation & purification/metabolism, Panax, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3867 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10247) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10247 | |||
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 | |
38509 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16498 | ||||
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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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 | |||
80741 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID10548.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118820 | Curators of the CIP | Collection of Institut Pasteur (CIP 104575) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104575 |