Strain identifier
BacDive ID: 11561
Type strain:
Species: Paenibacillus daejeonensis
Strain Designation: AP-20
Strain history: CIP <- 2003, JCM <- 2001, Lee, strain AP-20
NCBI tax ID(s): 1122917 (strain), 135193 (species)
General
@ref: 5955
BacDive-ID: 11561
DSM-Number: 15491
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, motile, rod-shaped
description: Paenibacillus daejeonensis AP-20 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1122917 | strain |
135193 | species |
strain history
@ref | history |
---|---|
5955 | <- K. S. Bae, Korea Research Inst. Bioscence and Biotechnol.; AP-20 |
67770 | J.-S. Lee AP-20. |
67771 | <- JS Lee, KRIBB |
118844 | CIP <- 2003, JCM <- 2001, Lee, strain AP-20 |
doi: 10.13145/bacdive11561.20230509.8.1
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 daejeonensis
- full scientific name: Paenibacillus daejeonensis Lee et al. 2002
@ref: 5955
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus daejeonensis
full scientific name: Paenibacillus daejeonensis Lee et al. 2002
strain designation: AP-20
type strain: yes
Morphology
cell morphology
@ref | cell shape | motility | flagellum arrangement | gram stain | confidence |
---|---|---|---|---|---|
67771 | rod-shaped | yes | peritrichous | ||
67771 | variable | ||||
69480 | yes | 98.26 | |||
69480 | positive | 100 | |||
118844 | rod-shaped | yes | positive |
colony morphology
- @ref: 118844
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5955 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
38232 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
118844 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5955 | positive | growth | 30 | mesophilic |
38232 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
118844 | positive | growth | 25-37 | mesophilic |
118844 | no | growth | 10 | psychrophilic |
118844 | no | growth | 22 | psychrophilic |
118844 | no | growth | 45 | thermophilic |
culture pH
- @ref: 118844
- ability: positive
- type: growth
- pH: 6
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
67771 | aerobe |
118844 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
118844 | NaCl | positive | growth | 2 % |
118844 | NaCl | no | growth | 0 % |
118844 | NaCl | no | growth | 4 % |
118844 | NaCl | no | growth | 6 % |
118844 | NaCl | no | growth | 8 % |
118844 | NaCl | no | growth | 10 % |
observation
@ref | observation |
---|---|
67770 | quinones: MK-7 |
67771 | 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 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
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 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
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 | 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 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
118844 | citrate | - | carbon source | 16947 |
118844 | esculin | + | hydrolysis | 4853 |
118844 | hippurate | + | hydrolysis | 606565 |
118844 | nitrate | - | reduction | 17632 |
118844 | nitrite | - | reduction | 16301 |
metabolite production
- @ref: 118844
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
118844 | 15688 | acetoin | - | |
118844 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
118844 | oxidase | + | |
118844 | beta-galactosidase | + | 3.2.1.23 |
118844 | alcohol dehydrogenase | - | 1.1.1.1 |
118844 | gelatinase | - | |
118844 | amylase | + | |
118844 | DNase | - | |
118844 | caseinase | - | 3.4.21.50 |
118844 | catalase | + | 1.11.1.6 |
118844 | tween esterase | - | |
118844 | gamma-glutamyltransferase | - | 2.3.2.2 |
118844 | lecithinase | - | |
118844 | lipase | - | |
118844 | lysine decarboxylase | - | 4.1.1.18 |
118844 | ornithine decarboxylase | - | 4.1.1.17 |
118844 | tryptophan deaminase | - | |
118844 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118844 | - | - | + | + | - | + | - | - | - | - | - | + | - | + | - | - | + | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118844 | - | - | - | +/- | - | - | - | - | +/- | +/- | - | - | - | - | +/- | - | - | +/- | - | - | - | +/- | - | - | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | - | - | +/- | +/- | +/- | - | +/- | +/- | - | - | - | +/- | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118844 | - | - | + | + | - | - | + | + | + | + | + | + | + | + | + | + | + | + | + | - | - | - | + | + | + | - | - | - | - | - | - | + | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
5955 | soil | Korea, Daejeon City | Republic of Korea | KOR | Asia |
67770 | Soil | Daejeon | Republic of Korea | KOR | Asia |
67771 | From soil | Daejeon | Republic of Korea | KOR | Asia |
118844 | Environment, Soil | Daejeon | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_122705.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_7719;97_9270;98_82527;99_122705&stattab=map
- Last taxonomy: Paenibacillus daejeonensis subclade
- 16S sequence: AF290916
- Sequence Identity:
- Total samples: 14
- soil counts: 5
- plant counts: 9
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
5955 | 1 | Risk group (German classification) |
118844 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 20218
- description: Paenibacillus daejeonensis strain AP-20 16S ribosomal RNA gene, partial sequence
- accession: AF290916
- length: 1465
- database: ena
- NCBI tax ID: 135193
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paenibacillus daejeonensis DSM 15491 | 1122917.3 | wgs | patric | 1122917 |
66792 | Paenibacillus daejeonensis DSM 15491 | 2519103188 | draft | img | 1122917 |
67770 | Paenibacillus daejeonensis DSM 15491 | GCA_000378385 | scaffold | ncbi | 1122917 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 53 | high performance liquid chromatography (HPLC) |
67771 | 53.0 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | yes | 89.129 | yes |
flagellated | yes | 87.123 | yes |
gram-positive | yes | 78.153 | yes |
anaerobic | no | 98.965 | no |
aerobic | yes | 91.629 | yes |
halophile | no | 81.034 | no |
spore-forming | yes | 92.686 | no |
glucose-util | yes | 92.144 | no |
glucose-ferment | no | 88.718 | no |
thermophile | no | 99.904 | yes |
External links
@ref: 5955
culture collection no.: DSM 15491, JCM 11236, KCTC 3745, BCRC 17345, CIP 107805
straininfo link
- @ref: 80789
- straininfo: 97892
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12508876 | Paenibacillus daejeonensis sp. nov., a novel alkaliphilic bacterium from soil. | Lee JS, Lee KC, Chang YH, Hong SG, Oh HW, Pyun YR, Bae KS | Int J Syst Evol Microbiol | 10.1099/00207713-52-6-2107 | 2002 | Bacillus/*classification/genetics/isolation & purification, Bacteria, Aerobic/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Terminology as Topic | Enzymology |
Phylogeny | 18768608 | Paenibacillus tarimensis sp. nov., isolated from sand in Xinjiang, China. | Wang M, Yang M, Zhou G, Luo X, Zhang L, Tang Y, Fang C | Int J Syst Evol Microbiol | 10.1099/ijs.0.65445-0 | 2008 | Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Gram-Positive Bacteria/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Silicon Dioxide, *Soil Microbiology, Spores, Bacterial/cytology, Temperature, Vitamin K 2/analysis | Genetics |
Phylogeny | 27503428 | Paenibacillus hispanicus sp. nov. isolated from Triticum aestivum roots. | Menendez E, Carro L, Tejedor C, Fernandez-Pascual M, Martinez-Molina E, Peix A, Velazquez E | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001401 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Triticum/*microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
5955 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15491) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15491 | |||
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 | |
38232 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5280 | ||||
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 | |||||
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 | |||
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 | |||
80789 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID97892.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118844 | Curators of the CIP | Collection of Institut Pasteur (CIP 107805) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107805 |