Strain identifier

BacDive ID: 11467

Type strain: Yes

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

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
59842species
1220560strain

strain history

@refhistory
1915<- NRRL <- N.R. Smith, 1351 (Bacillus circulans) <- F.E. Clark
67770NRRL NRS-1351 <-- N. R. Smith NRS-1351.
118255CIP <- 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

@refnamegrowthcompositionlink
35489MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
1915NUTRIENT AGAR (DSMZ Medium 1)yesName: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/1
118255CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
118255CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
1915positivegrowth30mesophilic
35489positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118255
  • oxygen tolerance: obligate aerobe

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371xylitol-builds acid from17151
68371inulin-builds acid from15443
68371D-sorbitol-builds acid from17924
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68368L-arabinose-fermentation30849
68368amygdalin+fermentation27613
68368melibiose+fermentation28053
68368sucrose+fermentation17992
68368L-rhamnose-fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol-fermentation17268
68368D-mannitol-fermentation16899
68368D-glucose+fermentation17634
68368gelatin+hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
118255nitrate-reduction17632
118255nitrite-reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11825535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23
118255oxidase+
118255catalase-1.11.1.6
118255urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118255--++-+----++-+++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARA
49272+--------+++----+++-

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
49272----+++--+-+++----+---+-+++++++++--+++-++---------
118255---+/-+/-+/---+/-+/-+/-+/-+/--+/--+/-+/--+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/--+/-+/----+/-+/----------

Isolation, sampling and environmental information

isolation

@refsample type
1915soil
49272Soil
67770Soil
118255Environment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
19151Risk group (German classification)
1182551Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paenibacillus chondroitinus clone JT-3F 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478105393ena59842
20218Paenibacillus chondroitinus partial 16S rRNA gene, isolate OS-213.aAM237395970ena59842
20218Paenibacillus chondroitinus DNA for 16S rRNAD820641417ena59842
20218Paenibacillus chondroitinus gene for 16S rRNA, partial sequenceAB0732061486ena59842
20218Paenibacillus chondroitinus gene for 16S rRNA, partial sequence, strain: NBRC 15376AB6808491461ena59842

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus chondroitinus NBRC 153761220560.3wgspatric1220560
67770Paenibacillus chondroitinus NBRC 15376GCA_004000765contigncbi1220560

GC content

@refGC-contentmethod
191545.1-46.0
6777047-48Buoyant density centrifugation (BD)
6777049Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes85.045no
gram-positiveyes79.095no
anaerobicno99.161no
aerobicyes87.397no
halophileno94.566no
spore-formingyes90.599no
glucose-utilyes89.166no
flagellatedyes87.039no
thermophileno99.777yes
glucose-fermentno91.595no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19502313Paenibacillus pectinilyticus sp. nov., isolated from the gut of Diestrammena apicalis.Park DS, Jeong WJ, Lee KH, Oh HW, Kim BC, Bae KS, Park HYInt J Syst Evol Microbiol10.1099/ijs.0.002261-02009Animals, 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, DNAGenetics
Phylogeny19654345Paenibacillus aestuarii sp. nov., isolated from an estuarine wetland.Bae JY, Kim KY, Kim JH, Lee K, Cho JC, Cha CJInt J Syst Evol Microbiol10.1099/ijs.0.011544-02009DNA, 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, WetlandsMetabolism
Phylogeny22535437Paenibacillus 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 WJAntonie Van Leeuwenhoek10.1007/s10482-012-9738-72012China, Molecular Sequence Data, Paenibacillus/classification/genetics/*isolation & purification, Soil/analysis, *Soil Microbiology, WetlandsGenetics
Phylogeny25313091Paenibacillus ferrarius sp. nov., isolated from iron mineral soil.Cao Y, Chen F, Li Y, Wei S, Wang GInt J Syst Evol Microbiol10.1099/ijs.0.063552-02014Bacterial 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/chemistryGenetics
Phylogeny25794481Paenibacillus alba nov., isolated from peat soil.Kim HS, Srinivasan S, Lee SSCurr Microbiol10.1007/s00284-015-0795-92015Aerobiosis, 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/analysisGenetics
Phylogeny27734255Paenibacillus oryzisoli sp. nov., isolated from the rhizosphere of rice.Zhang J, Ma XT, Gao JS, Zhang CW, Zhao JJ, Zhang RJ, Ma LA, Zhang XXAntonie Van Leeuwenhoek10.1007/s10482-016-0777-32016Base 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 MicrobiologyMetabolism
Phylogeny27995861Paenibacillus aceris sp. nov., isolated from the rhizosphere of Acer okamotoanum, a plant native to Ulleungdo Island, Republic of Korea.Hwang YJ, Ghim SYInt J Syst Evol Microbiol10.1099/ijsem.0.0017482017Acer/*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 MicrobiologyTranscriptome
Phylogeny32556479Paenibacillus anseongense sp. nov. a Silver Nanoparticle Producing Bacterium Isolated from Rhizospheric Soil.Huq MACurr Microbiol10.1007/s00284-020-02086-02020Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, *Metal Nanoparticles, *Paenibacillus/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silver, Soil, Soil MicrobiologyTranscriptome
Phylogeny33388935Paenibacillus silvestris sp. nov., Isolated from Forest Soil.Kim J, Jung HS, Baek JH, Chun BH, Khan SA, Jeon COCurr Microbiol10.1007/s00284-020-02333-42021Bacterial 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/analysisTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1915Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5051)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5051
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
35489Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14886
49272Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28527)https://www.ccug.se/strain?id=28527
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
80701Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10614.1StrainInfo: A central database for resolving microbial strain identifiers
118255Curators of the CIPCollection of Institut Pasteur (CIP 103123)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103123