Strain identifier

BacDive ID: 11581

Type strain: Yes

Species: Paenibacillus cookii

Strain Designation: B1718

Strain history: CIP <- 2003, N.A. Logan, Caledonian Univ., Glasgow, UK: strain B1718

NCBI tax ID(s): 157839 (species)

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General

@ref: 6661

BacDive-ID: 11581

DSM-Number: 16944

keywords: 16S sequence, Bacteria, facultative anaerobe, spore-forming, Gram-negative, motile, rod-shaped

description: Paenibacillus cookii B1718 is a facultative anaerobe, spore-forming, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 157839
  • Matching level: species

strain history

@refhistory
6661<- CIP
366902003, N.A. Logan, Caledonian Univ., Glasgow, UK: strain B1718
118741CIP <- 2003, N.A. Logan, Caledonian Univ., Glasgow, UK: strain B1718

doi: 10.13145/bacdive11581.20240510.9

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 cookii
  • full scientific name: Paenibacillus cookii Logan et al. 2004

@ref: 6661

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus cookii

full scientific name: Paenibacillus cookii Logan et al. 2004

strain designation: B1718

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
30123negative3.25 µm0.7 µmrod-shapedyes
118741positiverod-shapedyes

colony morphology

  • @ref: 118741

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6661CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l MnSO4 Distilled water
36690MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118741CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
6661positivegrowth30
30123positivegrowth15-50
30123positiveoptimum32.5
36690positivegrowth30
118741positivegrowth22-45
118741nogrowth10
118741nogrowth55

culture pH

@refabilitytypepHPH range
30123positivegrowth5.0-10alkaliphile
30123positiveoptimum7
118741positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30123facultative anaerobe
118741facultative anaerobe

spore formation

@refspore formation
30123yes
118741yes

halophily

@refsaltgrowthtested relationconcentration
30123NaClpositivegrowth5.0-7.0 %
30123NaClpositiveoptimum6 %
118741NaClpositivegrowth0-4 %
118741NaClnogrowth6 %
118741NaClnogrowth8 %
118741NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30123581435-dehydro-D-gluconate+carbon source
3012322599arabinose+carbon source
3012317057cellobiose+carbon source
3012328757fructose+carbon source
3012333984fucose+carbon source
3012328260galactose+carbon source
3012324265gluconate+carbon source
3012317234glucose+carbon source
3012317754glycerol+carbon source
3012328087glycogen+carbon source
3012317716lactose+carbon source
3012317306maltose+carbon source
3012337684mannose+carbon source
3012328053melibiose+carbon source
3012337657methyl D-glucoside+carbon source
30123506227N-acetylglucosamine+carbon source
3012316634raffinose+carbon source
3012333942ribose+carbon source
3012317814salicin+carbon source
3012317992sucrose+carbon source
3012327082trehalose+carbon source
3012318222xylose+carbon source
301234853esculin+hydrolysis
3012317632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837115443inulin-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
683714853esculin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose+builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11874116947citrate-carbon source
1187414853esculin+hydrolysis
118741606565hippurate+hydrolysis
11874117632nitrate+reduction
11874116301nitrite+reduction
11874117632nitrate+respiration

antibiotic resistance

  • @ref: 118741
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 118741
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11874115688acetoin-
11874117234glucose-

enzymes

@refvalueactivityec
30123catalase+1.11.1.6
30123gelatinase+
30123cytochrome oxidase+1.9.3.1
118741oxidase+
118741beta-galactosidase+3.2.1.23
118741alcohol dehydrogenase-1.1.1.1
118741gelatinase-
118741amylase-
118741caseinase-3.4.21.50
118741catalase+1.11.1.6
118741tween esterase-
118741gamma-glutamyltransferase-2.3.2.2
118741lecithinase-
118741lipase-
118741lysine decarboxylase-4.1.1.18
118741ornithine decarboxylase-4.1.1.17
118741protease-
118741urease-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
118741--++-+----++++-++-++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118741---+++--+/-+------------++/-++/-++++++/--+/-+/-++-++------+/-+/--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118741+-++--+++++++++++++++++--+-----+--++-----+--------------+---+--------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6661soilCandlemas Island,Lucifer hill, fumaroleUnited KingdomGBREurope
118741Environment, Soil, fumaroleLucifer hill, Candlemas IslandUnited KingdomGBREurope1998

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1403.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_812;97_946;98_1110;99_1403&stattab=map
  • Last taxonomy: Paenibacillus cookii
  • 16S sequence: AJ250317
  • Sequence Identity:
  • Total samples: 381
  • soil counts: 162
  • aquatic counts: 55
  • animal counts: 125
  • plant counts: 39

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
66611Risk group (German classification)
1187411Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6661
  • description: Bacterium LMG 18419 16S rRNA gene, strain LMG 18419
  • accession: AJ250317
  • length: 1495
  • database: nuccore
  • NCBI tax ID: 157839

GC content

  • @ref: 30123
  • GC-content: 51.6

External links

@ref: 6661

culture collection no.: DSM 16944, CIP 108110, LMG 18419, SSI 018, KCTC 3999

straininfo link

  • @ref: 80809
  • straininfo: 12008

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15280271Paenibacillus cineris sp. nov. and Paenibacillus cookii sp. nov., from Antarctic volcanic soils and a gelatin-processing plant.Logan NA, De Clerck E, Lebbe L, Verhelst A, Goris J, Forsyth G, Rodriguez-Diaz M, Heyndrickx M, De Vos PInt J Syst Evol Microbiol10.1099/ijs.0.02967-02004Aerobiosis, Antarctic Regions, Bacterial Proteins/analysis/isolation & purification, Bacterial Typing Techniques, DNA Fingerprinting, DNA, Bacterial/analysis/chemistry/isolation & purification, DNA, Ribosomal/analysis/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, *Gelatin, Genes, rRNA/genetics, Gram-Positive Endospore-Forming Bacteria/*classification/cytology/isolation & purification/physiology, *Industrial Microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polymorphism, Restriction Fragment Length, Proteome/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, *Soil MicrobiologyEnzymology
Phylogeny29858827Paenibacillus albilobatus sp. nov., isolated from acidic soil on Jeju Island.Lee JW, Kim YE, Kang MS, Lee KE, Lee EY, Park SJJ Microbiol10.1007/s12275-018-8158-42018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Islands, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/*isolation & purification/physiology, Phenotype, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride, Soil, *Soil Microbiology, Species Specificity, TemperaturePhenotype

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6661Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16944)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16944
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
30123Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2647728776041
36690Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5697
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João 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
80809Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12008.1StrainInfo: A central database for resolving microbial strain identifiers
118741Curators of the CIPCollection of Institut Pasteur (CIP 108110)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108110