Strain identifier
BacDive ID: 11545
Type strain:
Species: Paenibacillus chibensis
Strain Designation: B-142
Strain history: CIP <- 1997, O. Shida, Res. Lab., Higeta Shoyu Co, Chiba, Japan: strain HSCC 442 <- NRRL: strain B-142 <- FDA
NCBI tax ID(s): 59846 (species)
General
@ref: 4462
BacDive-ID: 11545
DSM-Number: 11731
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, motile
description: Paenibacillus chibensis B-142 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 59846
- Matching level: species
strain history
@ref | history |
---|---|
4462 | <- O. Shida, Higeta Shoyu; HSCC 442 <- NRRL <- FDA; PCI 221 |
67770 | HSCC 442 <-- NRRL B-142 <-- FDA strain PCI 221. |
118231 | CIP <- 1997, O. Shida, Res. Lab., Higeta Shoyu Co, Chiba, Japan: strain HSCC 442 <- NRRL: strain B-142 <- FDA |
doi: 10.13145/bacdive11545.20230509.8.1
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 chibensis
- full scientific name: Paenibacillus chibensis Shida et al. 1997
@ref: 4462
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus chibensis
full scientific name: Paenibacillus chibensis Shida et al. 1997
strain designation: B-142
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 92.823 | ||
69480 | 100 | positive | ||
118231 | yes | positive | rod-shaped |
colony morphology
- @ref: 118231
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4462 | 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 |
35797 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
118231 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4462 | positive | growth | 30 | mesophilic |
35797 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
118231 | positive | growth | 22-45 | |
118231 | no | growth | 10 | psychrophilic |
118231 | no | growth | 55 | thermophilic |
culture pH
- @ref: 118231
- ability: positive
- type: growth
- pH: 6
Physiology and metabolism
oxygen tolerance
- @ref: 118231
- oxygen tolerance: facultative anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
118231 | yes |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
118231 | NaCl | positive | growth | 0-4 % |
118231 | NaCl | no | growth | 6 % |
118231 | NaCl | no | growth | 8 % |
118231 | NaCl | no | growth | 10 % |
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 | 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 | 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 | trehalose | + | builds acid from | 27082 |
68371 | sucrose | + | builds acid from | 17992 |
68371 | melibiose | + | builds acid from | 28053 |
68371 | lactose | + | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | + | builds acid from | 17057 |
68371 | salicin | + | builds acid from | 17814 |
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 | D-mannitol | + | builds acid from | 16899 |
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 | 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 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
118231 | esculin | + | hydrolysis | 4853 |
118231 | hippurate | - | hydrolysis | 606565 |
118231 | nitrate | + | reduction | 17632 |
118231 | nitrite | - | reduction | 16301 |
118231 | nitrate | + | respiration | 17632 |
metabolite production
- @ref: 118231
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
118231 | 15688 | acetoin | - | |
118231 | 17234 | glucose | + |
enzymes
@ref | value | activity | ec |
---|---|---|---|
118231 | oxidase | + | |
118231 | beta-galactosidase | + | 3.2.1.23 |
118231 | alcohol dehydrogenase | - | 1.1.1.1 |
118231 | gelatinase | - | |
118231 | amylase | + | |
118231 | DNase | - | |
118231 | caseinase | - | 3.4.21.50 |
118231 | catalase | + | 1.11.1.6 |
118231 | tween esterase | - | |
118231 | gamma-glutamyltransferase | - | 2.3.2.2 |
118231 | lecithinase | - | |
118231 | lipase | - | |
118231 | lysine decarboxylase | - | 4.1.1.18 |
118231 | ornithine decarboxylase | - | 4.1.1.17 |
118231 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118231 | - | - | + | + | - | + | - | - | - | - | + | + | + | + | - | + | + | + | - | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118231 | - | - | - | +/- | + | + | - | - | + | + | + | + | + | - | +/- | - | - | + | - | - | - | +/- | + | + | +/- | + | + | + | + | + | + | + | +/- | - | + | + | + | - | + | + | - | - | - | +/- | - | - | +/- | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118231 | + | + | + | + | + | - | + | + | + | + | + | + | + | + | - | + | - | + | + | + | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
4462 | soil | USA | USA | North America |
67770 | Soil |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
4462 | 1 | Risk group (German classification) |
118231 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Paenibacillus chibensis gene for 16S rRNA, partial sequence | AB073194 | 1505 | ena | 59846 |
20218 | Paenibacillus chibensis gene for 16S rRNA, partial sequence, strain: NBRC 15958 | AB681006 | 1480 | ena | 59846 |
20218 | B.amylolyticus 16S ribosomal RNA | X60606 | 1435 | ena | 1451 |
20218 | Paenibacillus chibensis DNA for 16S rRNA | D85395 | 1436 | ena | 59846 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paenibacillus chibensis strain NBRC 15958 | 59846.3 | wgs | patric | 59846 |
66792 | Paenibacillus chibensis NBRC 15958 | 2925295060 | draft | img | 59846 |
67770 | Paenibacillus chibensis NBRC 15958 | GCA_004001045 | contig | ncbi | 59846 |
GC content
- @ref: 67770
- GC-content: 52.8
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | yes | 79.49 | no |
anaerobic | no | 98.579 | no |
halophile | no | 93.971 | no |
spore-forming | yes | 96.869 | no |
glucose-util | yes | 89.848 | no |
thermophile | no | 98.359 | yes |
flagellated | yes | 76.246 | no |
aerobic | yes | 80.955 | no |
motile | yes | 88.775 | no |
glucose-ferment | no | 83.425 | no |
External links
@ref: 4462
culture collection no.: DSM 11731, IFO 15958, JCM 9905, NBRC 15958, NRRL B-142, HSCC 442, PCI 221, ATCC 9966, ATCC BAA 725, CCM 1084, CECT 375, CIP 105254, IAM 1112, IFO 3329, KCTC 3758, LMG 14457, NBRC 3329, NCIMB 8144
straininfo link
- @ref: 80775
- straininfo: 9916
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 21887645 | Paenibacillus telluris sp. nov., a novel phosphate-solubilizing bacterium isolated from soil. | Lee JC, Kim CJ, Yoon KH | J Microbiol | 10.1007/s12275-011-0471-0 | 2011 | Bacterial Typing Techniques, Base Composition, Base Sequence, DNA, Bacterial, Fatty Acids/chemistry, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/ultrastructure, Phenotype, Phosphates/*chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Solubility | Genetics |
Phylogeny | 24556633 | Paenibacillus shirakamiensis sp. nov., isolated from the trunk surface of a Japanese oak (Quercus crispula). | Tonouchi A, Tazawa D, Fujita T | Int J Syst Evol Microbiol | 10.1099/ijs.0.055772-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Molecular Sequence Data, Paenibacillus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Plant Stems/microbiology, Quercus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 26373452 | Paenibacillus zeae sp. nov., isolated from maize (Zea mays L.) seeds. | Liu Y, Zhai L, Wang R, Zhao R, Zhang X, Chen C, Cao Y, Cao Y, Xu T, Ge Y, Zhao J, Cheng C | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000608 | 2015 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seeds/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiology | Enzymology |
Phylogeny | 27498790 | Paenibacillus solani sp. nov., isolated from potato rhizosphere soil. | Liu B, Liu GH, Sengonca C, Schumann P, Lan JL, Chen DJ, Cui WD, Lin NQ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001378 | 2016 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Solanum tuberosum/*microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 33595431 | Description of Paenibacillus dokdonensis sp. nov., a new bacterium isolated from soil. | Paek J, Bai L, Shin Y, Kim H, Kook JK, Chang YH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004707 | 2021 | ||
Metabolism | 34822536 | Antifungal Activity of Biocontrol Agents In Vitro and Potential Application to Reduce Mycotoxins (Aflatoxin B1 and Ochratoxin A). | Illueca F, Vila-Donat P, Calpe J, Luz C, Meca G, Quiles JM | Toxins (Basel) | 10.3390/toxins13110752 | 2021 | Aflatoxin B1/*metabolism, Antifungal Agents/*pharmacology, Bacillus amyloliquefaciens/metabolism, Cell-Free System, Fungicides, Industrial/*pharmacology, In Vitro Techniques, Ochratoxins/*metabolism, Paenibacillus/metabolism, Pantoea/metabolism, *Pest Control, Biological, Poisons/*metabolism | Biotechnology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4462 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11731) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11731 | |||
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 | |
35797 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17253 | ||||
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/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
80775 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID9916.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118231 | Curators of the CIP | Collection of Institut Pasteur (CIP 105254) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105254 |