Strain identifier
BacDive ID: 11467
Type strain:
Species: Paenibacillus chondroitinus
Strain Designation: 1351
Strain history: CIP <- 1988, L.K. Nakamura, NRRL <- N.R. Smith: strain NRS-1351, Bacillus circulans <- F.E. Clark
NCBI tax ID(s): 1220560 (strain), 59842 (species)
General
@ref: 1915
BacDive-ID: 11467
DSM-Number: 5051
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Paenibacillus chondroitinus 1351 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.
NCBI tax id
NCBI tax id | Matching level |
---|---|
59842 | species |
1220560 | strain |
strain history
@ref | history |
---|---|
1915 | <- NRRL <- N.R. Smith, 1351 (Bacillus circulans) <- F.E. Clark |
67770 | NRRL NRS-1351 <-- N. R. Smith NRS-1351. |
118255 | CIP <- 1988, L.K. Nakamura, NRRL <- N.R. Smith: strain NRS-1351, Bacillus circulans <- F.E. Clark |
doi: 10.13145/bacdive11467.20230509.8.1
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 chondroitinus
- full scientific name: Paenibacillus chondroitinus (Nakamura 1987) Shida et al. 1997
synonyms
- @ref: 20215
- synonym: Bacillus chondroitinus
@ref: 1915
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus chondroitinus
full scientific name: Paenibacillus chondroitinus (Nakamura 1987) Shida et al. 1997
strain designation: 1351
type strain: yes
Morphology
cell morphology
- @ref: 118255
- gram stain: negative
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
35489 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
1915 | NUTRIENT AGAR (DSMZ Medium 1) | yes | 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 | https://mediadive.dsmz.de/medium/1 |
118255 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
118255 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1915 | positive | growth | 30 | mesophilic |
35489 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 118255
- oxygen tolerance: obligate aerobe
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 | xylitol | - | builds acid from | 17151 |
68371 | inulin | - | builds acid from | 15443 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
68368 | L-arabinose | - | fermentation | 30849 |
68368 | amygdalin | + | fermentation | 27613 |
68368 | melibiose | + | fermentation | 28053 |
68368 | sucrose | + | fermentation | 17992 |
68368 | L-rhamnose | - | fermentation | 62345 |
68368 | sorbitol | - | fermentation | 30911 |
68368 | myo-inositol | - | fermentation | 17268 |
68368 | D-mannitol | - | fermentation | 16899 |
68368 | D-glucose | + | fermentation | 17634 |
68368 | gelatin | + | hydrolysis | 5291 |
68368 | tryptophan | - | energy source | 27897 |
68368 | urea | - | hydrolysis | 16199 |
68368 | citrate | - | assimilation | 16947 |
68368 | ornithine | - | degradation | 18257 |
68368 | lysine | - | degradation | 25094 |
68368 | arginine | - | hydrolysis | 29016 |
118255 | nitrate | - | reduction | 17632 |
118255 | nitrite | - | reduction | 16301 |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
118255 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | + | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
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 |
118255 | oxidase | + | |
118255 | catalase | - | 1.11.1.6 |
118255 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118255 | - | - | + | + | - | + | - | - | - | - | + | + | - | + | + | + | - | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
49272 | + | - | - | - | - | - | - | - | - | + | + | + | - | - | - | - | + | + | + | - |
API 50CHac
@ref | Q | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
49272 | - | - | - | - | + | + | + | - | - | + | - | + | + | + | - | - | - | - | + | - | - | - | + | - | + | + | + | + | + | + | + | + | + | - | - | + | + | + | - | + | + | - | - | - | - | - | - | - | - | - |
118255 | - | - | - | +/- | +/- | +/- | - | - | +/- | +/- | +/- | +/- | +/- | - | +/- | - | +/- | +/- | - | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | - | +/- | +/- | - | - | - | +/- | +/- | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
1915 | soil |
49272 | Soil |
67770 | Soil |
118255 | Environment, Soil |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
1915 | 1 | Risk group (German classification) |
118255 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Paenibacillus chondroitinus clone JT-3F 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | AF478105 | 393 | ena | 59842 |
20218 | Paenibacillus chondroitinus partial 16S rRNA gene, isolate OS-213.a | AM237395 | 970 | ena | 59842 |
20218 | Paenibacillus chondroitinus DNA for 16S rRNA | D82064 | 1417 | ena | 59842 |
20218 | Paenibacillus chondroitinus gene for 16S rRNA, partial sequence | AB073206 | 1486 | ena | 59842 |
20218 | Paenibacillus chondroitinus gene for 16S rRNA, partial sequence, strain: NBRC 15376 | AB680849 | 1461 | ena | 59842 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paenibacillus chondroitinus NBRC 15376 | 1220560.3 | wgs | patric | 1220560 |
67770 | Paenibacillus chondroitinus NBRC 15376 | GCA_004000765 | contig | ncbi | 1220560 |
GC content
@ref | GC-content | method |
---|---|---|
1915 | 45.1-46.0 | |
67770 | 47-48 | Buoyant density centrifugation (BD) |
67770 | 49 | Buoyant density centrifugation (BD) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 85.045 | no |
gram-positive | yes | 79.095 | no |
anaerobic | no | 99.161 | no |
aerobic | yes | 87.397 | no |
halophile | no | 94.566 | no |
spore-forming | yes | 90.599 | no |
glucose-util | yes | 89.166 | no |
flagellated | yes | 87.039 | no |
thermophile | no | 99.777 | yes |
glucose-ferment | no | 91.595 | no |
External links
@ref: 1915
culture collection no.: DSM 5051, NRRL NRS-1351, CCUG 28527, JCM 9072, ATCC 51184, CCM 4538, CIP 103123, IFO 15376, KCTC 3568, LMG 18040, NBRC 15376, NCIMB 12518, NRRL: NRS-1351
straininfo link
- @ref: 80701
- straininfo: 10614
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19502313 | Paenibacillus pectinilyticus sp. nov., isolated from the gut of Diestrammena apicalis. | Park DS, Jeong WJ, Lee KH, Oh HW, Kim BC, Bae KS, Park HY | Int J Syst Evol Microbiol | 10.1099/ijs.0.002261-0 | 2009 | Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Gastrointestinal Tract/*microbiology, Genotype, Gram-Positive Endospore-Forming Rods/*classification/genetics/isolation & purification/physiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Orthoptera/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Phylogeny | 19654345 | Paenibacillus aestuarii sp. nov., isolated from an estuarine wetland. | Bae JY, Kim KY, Kim JH, Lee K, Cho JC, Cha CJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.011544-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Wetlands | Metabolism |
Phylogeny | 22535437 | Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China. | Ming H, Nie GX, Jiang HC, Yu TT, Zhou EM, Feng HG, Tang SK, Li WJ | Antonie Van Leeuwenhoek | 10.1007/s10482-012-9738-7 | 2012 | China, Molecular Sequence Data, Paenibacillus/classification/genetics/*isolation & purification, Soil/analysis, *Soil Microbiology, Wetlands | Genetics |
Phylogeny | 25313091 | Paenibacillus ferrarius sp. nov., isolated from iron mineral soil. | Cao Y, Chen F, Li Y, Wei S, Wang G | Int J Syst Evol Microbiol | 10.1099/ijs.0.063552-0 | 2014 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Iron/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 25794481 | Paenibacillus alba nov., isolated from peat soil. | Kim HS, Srinivasan S, Lee SS | Curr Microbiol | 10.1007/s00284-015-0795-9 | 2015 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Locomotion, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, Soil, *Soil Microbiology, Vitamin K 2/analysis | Genetics |
Phylogeny | 27734255 | Paenibacillus oryzisoli sp. nov., isolated from the rhizosphere of rice. | Zhang J, Ma XT, Gao JS, Zhang CW, Zhao JJ, Zhang RJ, Ma LA, Zhang XX | Antonie Van Leeuwenhoek | 10.1007/s10482-016-0777-3 | 2016 | Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Oryza/growth & development, Paenibacillus/classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, *Soil Microbiology | Metabolism |
Phylogeny | 27995861 | Paenibacillus aceris sp. nov., isolated from the rhizosphere of Acer okamotoanum, a plant native to Ulleungdo Island, Republic of Korea. | Hwang YJ, Ghim SY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001748 | 2017 | Acer/*microbiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Islands, Paenibacillus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology | Transcriptome |
Phylogeny | 32556479 | Paenibacillus anseongense sp. nov. a Silver Nanoparticle Producing Bacterium Isolated from Rhizospheric Soil. | Huq MA | Curr Microbiol | 10.1007/s00284-020-02086-0 | 2020 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, *Metal Nanoparticles, *Paenibacillus/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silver, Soil, Soil Microbiology | Transcriptome |
Phylogeny | 33388935 | Paenibacillus silvestris sp. nov., Isolated from Forest Soil. | Kim J, Jung HS, Baek JH, Chun BH, Khan SA, Jeon CO | Curr Microbiol | 10.1007/s00284-020-02333-4 | 2021 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Forests, *Paenibacillus/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil, Vitamin K 2/analysis | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1915 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5051) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5051 | |||
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 | |
35489 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/14886 | ||||
49272 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 28527) | https://www.ccug.se/strain?id=28527 | |||
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 | |||||
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
80701 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID10614.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118255 | Curators of the CIP | Collection of Institut Pasteur (CIP 103123) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103123 |