Strain identifier

BacDive ID: 11585

Type strain: Yes

Species: Paenibacillus barcinonensis

Strain Designation: BP-23

Strain history: CIP <- 2005, CECT <- strain BP-23

NCBI tax ID(s): 198119 (species)

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General

@ref: 5948

BacDive-ID: 11585

DSM-Number: 15478

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive, rod-shaped

description: Paenibacillus barcinonensis BP-23 is an anaerobe, spore-forming, mesophilic bacterium of the family Paenibacillaceae.

NCBI tax id

  • NCBI tax id: 198119
  • Matching level: species

strain history

@refhistory
5948<- M. Sánchez, Univ. Barcelona; BP23
116733CIP <- 2005, CECT <- strain BP-23

doi: 10.13145/bacdive11585.20230509.8.1

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 barcinonensis
  • full scientific name: Paenibacillus barcinonensis Sánchez et al. 2005

@ref: 5948

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus barcinonensis

full scientific name: Paenibacillus barcinonensis Sánchez et al. 2005

strain designation: BP-23

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31353positive3 µm0.75 µmrod-shaped
116733positiverod-shapedyes

colony morphology

  • @ref: 116733
  • hemolysis ability: 1

pigmentation

  • @ref: 31353
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5948CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
38299MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116733CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5948positivegrowth30mesophilic
31353positivegrowth10-40
31353positiveoptimum25mesophilic
38299positivegrowth30mesophilic
116733positivegrowth10-45
116733nogrowth55thermophilic

culture pH

@refabilitytypepHPH range
31353positivegrowth5-10.4alkaliphile
31353positiveoptimum7.7
116733positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31353anaerobe
116733facultative anaerobe

spore formation

@refspore formation
31353yes
116733yes

halophily

@refsaltgrowthtested relationconcentration
31353NaClpositivegrowth<5 %
31353NaClpositiveoptimum2.5 %
116733NaClpositivegrowth0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3135322599arabinose+carbon source
3135317057cellobiose+carbon source
3135328757fructose+carbon source
3135328260galactose+carbon source
3135324265gluconate+carbon source
3135317234glucose+carbon source
3135317754glycerol+carbon source
3135317716lactose+carbon source
3135317306maltose+carbon source
3135329864mannitol+carbon source
3135337684mannose+carbon source
3135328053melibiose+carbon source
31353506227N-acetylglucosamine+carbon source
3135316634raffinose+carbon source
3135333942ribose+carbon source
3135317814salicin+carbon source
3135317992sucrose+carbon source
3135327082trehalose+carbon source
3135318222xylose+carbon source
313534853esculin+hydrolysis
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+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
6837116634raffinose+builds acid from
683716731melezitose+builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+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
6837174863methyl beta-D-xylopyranoside+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
11673316947citrate-carbon source
1167334853esculin+hydrolysis
11673317632nitrate-reduction
11673316301nitrite-reduction
11673317632nitrate+respiration

metabolite production

  • @ref: 116733
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11673315688acetoin-
11673317234glucose+

enzymes

@refvalueactivityec
31353catalase+1.11.1.6
116733oxidase+
116733beta-galactosidase+3.2.1.23
116733alcohol dehydrogenase-1.1.1.1
116733gelatinase+
116733amylase-
116733DNase+
116733caseinase+3.4.21.50
116733catalase+1.11.1.6
116733tween esterase+
116733gamma-glutamyltransferase-2.3.2.2
116733lecithinase-
116733lipase-
116733lysine decarboxylase-4.1.1.18
116733ornithine decarboxylase-4.1.1.17
116733protease+
116733urease-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
116733-+++-+--++++++-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116733+-++++--+++++-+-++-+/-++++++++++++-++---++---+--+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116733+++-+-++++++++++++-++++--+-----+-+++-------------------+---++--------------------------------------

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample typegeographic location
5948SpainESPEurope
116733SpainESPEuropeEnvironment, Soil, rice fieldIsbro delta

taxonmaps

  • @ref: 69479
  • File name: preview.99_41118.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_141;97_15017;98_29427;99_41118&stattab=map
  • Last taxonomy: Paenibacillus
  • 16S sequence: AJ716019
  • Sequence Identity:
  • Total samples: 530
  • soil counts: 116
  • aquatic counts: 28
  • animal counts: 92
  • plant counts: 294

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59481Risk group (German classification)
1167331Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31353
  • description: Paenibacillus barcinonensis 16S rRNA gene, type strain BP-23T
  • accession: AJ716019
  • length: 1523
  • database: nuccore
  • NCBI tax ID: 198119

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus barcinonensis CECT 7022GCA_003217495scaffoldncbi198119
66792Paenibacillus barcinonensis strain CECT 7022198119.4wgspatric198119
66792Paenibacillus barcinonensis CECT 70222770939580draftimg198119

GC content

  • @ref: 31353
  • GC-content: 45

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes70.714no
gram-positiveyes85.041yes
anaerobicno95.056yes
halophileno84.496no
spore-formingyes95.646yes
aerobicyes81.866yes
glucose-utilyes93.538yes
thermophileno99.823no
motileyes83.734no
glucose-fermentno83.575no

External links

@ref: 5948

culture collection no.: DSM 15478, CECT 7022, CIP 108718

straininfo link

  • @ref: 80813
  • straininfo: 138020

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774688Paenibacillus barcinonensis sp. nov., a xylanase-producing bacterium isolated from a rice field in the Ebro River delta.Sanchez MM, Fritze D, Blanco A, Sproer C, Tindall BJ, Schumann P, Kroppenstedt RM, Diaz P, Pastor FIJInt J Syst Evol Microbiol10.1099/ijs.0.63383-02005DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Endo-1,4-beta Xylanases/*metabolism, Genes, rRNA, Gram-Positive Endospore-Forming Rods/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rivers, Sequence Analysis, DNA, *Soil Microbiology, SpainGenetics
Phylogeny18319478Paenibacillus provencensis sp. nov., isolated from human cerebrospinal fluid, and Paenibacillus urinalis sp. nov., isolated from human urine.Roux V, Fenner L, Raoult DInt J Syst Evol Microbiol10.1099/ijs.0.65228-02008Adult, Bacterial Typing Techniques, Cerebrospinal Fluid/*microbiology, DNA, Bacterial/analysis, Fatty Acids/analysis, Female, Genes, rRNA, Genotype, Gram-Negative Bacteria/*classification/genetics/*isolation & purification, Gram-Negative Bacterial Infections/*microbiology, Humans, Male, Middle Aged, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Urine/*microbiologyGenetics
Phylogeny22467156Paenibacillus oceanisediminis sp. nov. isolated from marine sediment.Lee J, Shin NR, Jung MJ, Roh SW, Kim MS, Lee JS, Lee KC, Kim YO, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.037085-02012Aquaculture, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Enzymology24549767Xyn11E from Paenibacillus barcinonensis BP-23: a LppX-chaperone-dependent xylanase with potential for upgrading paper pulps.Valenzuela SV, Diaz P, Pastor FIAppl Microbiol Biotechnol10.1007/s00253-014-5565-22014Cloning, Molecular, DNA, Bacterial/chemistry/genetics, Escherichia coli/genetics/metabolism, Gene Expression, Hydrogen-Ion Concentration, Isoelectric Point, Kinetics, Molecular Sequence Data, Molecular Weight, Paenibacillus/*enzymology/genetics, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Sequence Analysis, DNA, Substrate Specificity, Temperature, Xylosidases/chemistry/*genetics/isolation & purification/*metabolismMetabolism
Metabolism24929101Unusual carboxylesterase bearing a GGG(A)X-type oxyanion hole discovered in Paenibacillus barcinonensis BP-23.Infanzon B, Valenzuela SV, Fillat A, Pastor FI, Diaz PBiochimie10.1016/j.biochi.2014.06.0032014Alcohols/metabolism, Amino Acid Motifs, Carboxylesterase/*chemistry/genetics/*metabolism, Cloning, Molecular, Conserved Sequence, Paenibacillus/*enzymology, Peptide Hydrolases/metabolism, PhylogenyEnzymology
Metabolism25603884New GH16 beta-glucanase from Paenibacillus barcinonensis BP-23 releases a complex pattern of mixed-linkage oligomers from barley glucan.Cerda LA, Valenzuela SV, Diaz P, Pastor FIBiotechnol Appl Biochem10.1002/bab.13482015Cloning, Molecular, Glucans/chemistry/*metabolism, Glycoside Hydrolases/chemistry/genetics/*metabolism, Hordeum/chemistry/*metabolism, Hydrolysis, Paenibacillus/chemistry/*enzymology/genetics/metabolism, Recombinant Proteins/chemistry/genetics/metabolismEnzymology
Phylogeny26721586Paenibacillus puernese sp. nov., a beta-glucosidase-producing bacterium isolated from Pu'er tea.Wang DD, Kim YJ, Hoang VA, Nguyen NL, Singh P, Wang C, Chun-Yang DArch Microbiol10.1007/s00203-015-1180-62015Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, *Food Microbiology, Glucosidases/metabolism, Paenibacillus/*classification/enzymology/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species SpecificityBiotechnology
Metabolism27316951The Glycoside Hydrolase Family 8 Reducing-End Xylose-Releasing Exo-oligoxylanase Rex8A from Paenibacillus barcinonensis BP-23 Is Active on Branched Xylooligosaccharides.Valenzuela SV, Lopez S, Biely P, Sanz-Aparicio J, Pastor FIAppl Environ Microbiol10.1128/AEM.01329-162016Bacterial Proteins/chemistry/genetics/*metabolism, Catalytic Domain, Glucuronates/chemistry/*metabolism, Glycoside Hydrolases/chemistry/genetics/*metabolism, Multigene Family, Oligosaccharides/chemistry/*metabolism, Paenibacillus/chemistry/*enzymology/genetics, Substrate Specificity, Xylose/*metabolism, Xylosidases/genetics/*metabolismEnzymology
Phylogeny27902310Paenibacillus silvae sp. nov., isolated from a tropical rainforest soil.Huang H, Zhang F, Liu M, Cui Y, Sun Q, Zhu J, Zou X, Bao SInt J Syst Evol Microbiol10.1099/ijsem.0.0016082017Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rainforest, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny28671536Paenibacillus polysaccharolyticus sp. nov., a xylanolytic and cellulolytic bacteria isolated from leaves of Bamboo Phyllostachys aureosulcata.Madhaiyan M, Poonguzhali S, Saravanan VS, Duraipandiyan V, Al-Dhabi NA, Kwon SW, Whitman WBInt J Syst Evol Microbiol10.1099/ijsem.0.0019012017Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Plant Leaves/*microbiology, Poaceae/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Metabolism32352213Structural analysis of the reducing-end xylose-releasing exo-oligoxylanase Rex8A from Paenibacillus barcinonensis BP-23 deciphers its molecular specificity.Jimenez-Ortega E, Valenzuela S, Ramirez-Escudero M, Pastor FJ, Sanz-Aparicio JFEBS J10.1111/febs.153322020Amino Acid Sequence, Bacterial Proteins/*chemistry/*metabolism, Crystallization, Crystallography, X-Ray, Paenibacillus/*enzymology, Protein Conformation, Sequence Homology, Substrate Specificity, Xylose/*metabolism, Xylosidases/*chemistry/*metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
5948Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15478)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15478
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
31353Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2766628776041
38299Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6378
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)
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
80813Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138020.1StrainInfo: A central database for resolving microbial strain identifiers
116733Curators of the CIPCollection of Institut Pasteur (CIP 108718)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108718