Strain identifier

BacDive ID: 11609

Type strain: Yes

Species: Paenibacillus mendelii

Strain Designation: C/2

Strain history: CIP <- 2005, CCM <- 2000, T. Sobek: strain C/2, Bacillus sp.

NCBI tax ID(s): 206163 (species)

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General

@ref: 7907

BacDive-ID: 11609

DSM-Number: 19248

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

description: Paenibacillus mendelii C/2 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from seed of Pisum sativum cv. Cesar.

NCBI tax id

  • NCBI tax id: 206163
  • Matching level: species

strain history

@refhistory
7907<- CCM <- T. Sobek, strain C/2
120891CIP <- 2005, CCM <- 2000, T. Sobek: strain C/2, Bacillus sp.

doi: 10.13145/bacdive11609.20230509.8.1

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 mendelii
  • full scientific name: Paenibacillus mendelii Smerda et al. 2005

@ref: 7907

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus mendelii

full scientific name: Paenibacillus mendelii Smerda et al. 2005

strain designation: C/2

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31536variablerod-shaped
69480yes97.085
69480positive100
120891positiverod-shapedno

colony morphology

  • @ref: 120891

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7907CASO 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
7907NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
40112MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120891CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7907positivegrowth30mesophilic
31536positivegrowth25-30mesophilic
31536positiveoptimum27.5mesophilic
40112positivegrowth37mesophilic

culture pH

  • @ref: 31536
  • ability: positive
  • type: optimum
  • pH: 8.5
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31536facultative anaerobe
120891obligate aerobe

spore formation

@refspore formationconfidence
31536yes
69481yes100
69480yes100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3153622599arabinose+carbon source
3153617057cellobiose+carbon source
3153628757fructose+carbon source
3153633984fucose+carbon source
3153628260galactose+carbon source
3153624265gluconate+carbon source
3153617234glucose+carbon source
3153617754glycerol+carbon source
3153617716lactose+carbon source
3153617306maltose+carbon source
3153628053melibiose+carbon source
3153616634raffinose+carbon source
3153626546rhamnose+carbon source
3153633942ribose+carbon source
3153617814salicin+carbon source
3153617992sucrose+carbon source
3153627082trehalose+carbon source
3153618222xylose+carbon source
315364853esculin+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
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837115443inulin-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
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
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
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
12089117632nitrate-reduction
12089116301nitrite-reduction

metabolite production

  • @ref: 120891
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31536catalase+1.11.1.6
31536cytochrome oxidase+1.9.3.1
120891oxidase-
120891alcohol dehydrogenase-1.1.1.1
120891catalase+1.11.1.6
120891lysine decarboxylase-4.1.1.18
120891ornithine decarboxylase-4.1.1.17
120891urease-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
120891--++-----+++++-+-+-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120891+-+/-+/-++--++/-+/----+----++++-++++++/-+/-+/--+/-+/-+/---++/-+/-+/-+/-+----+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7907seed of Pisum sativum cv. CesarSouthern MoraviaCzech RepublicCZEEurope
120891Seed, Pisum sativum cv. CesarSouthern MoraviaCzech RepublicCZEEurope

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Fruit (Seed)

taxonmaps

  • @ref: 69479
  • File name: preview.99_86964.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_8055;97_9958;98_60147;99_86964&stattab=map
  • Last taxonomy: Paenibacillus mendelii subclade
  • 16S sequence: AF537343
  • Sequence Identity:
  • Total samples: 95
  • soil counts: 68
  • aquatic counts: 10
  • animal counts: 3
  • plant counts: 14

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
79071Risk group (German classification)
1208911Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7907
  • description: Paenibacillus mendelii strain C/2 16S ribosomal RNA gene, partial sequence
  • accession: AF537343
  • length: 1543
  • database: ena
  • NCBI tax ID: 206163

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus mendelii strain DSM 19248206163.3wgspatric206163
66792Paenibacillus mendelii DSM 192482901065067draftimg206163
66792Paenibacillus mendelii C/2GCA_024498075scaffoldncbi206163

GC content

  • @ref: 7907
  • GC-content: 50.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes84.499no
gram-positiveyes84.864no
anaerobicno99.168yes
aerobicyes87.767yes
halophileno97.553no
spore-formingyes96.414no
glucose-utilyes90.72yes
flagellatedyes80.626no
thermophileno99.172yes
glucose-fermentno91.106no

External links

@ref: 7907

culture collection no.: DSM 19248, CCM 4839, LMG 23002, CIP 109077

straininfo link

  • @ref: 80835
  • straininfo: 137488

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280495Paenibacillus mendelii sp. nov., from surface-sterilized seeds of Pisum sativum L.Smerda J, Sedlacek I, Pacova Z, Durnova E, Smiskova A, Havel LInt J Syst Evol Microbiol10.1099/ijs.0.63759-02005Base Composition, DNA, Bacterial/analysis/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gram-Positive Bacteria/*classification/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peas/*microbiology, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Seeds/*microbiology, Sequence Analysis, DNAEnzymology
Phylogeny17012558Paenibacillus sepulcri sp. nov., isolated from biodeteriorated mural paintings in the Servilia tomb.Smerda J, Sedlacek I, Pacova Z, Krejci E, Havel LInt J Syst Evol Microbiol10.1099/ijs.0.64280-02006Bacteria, Anaerobic/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Burial, DNA, Bacterial/analysis, Endospore-Forming Bacteria/classification/genetics/isolation & purification/physiology, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, *Paintings, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Spores, Bacterial/physiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7907Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19248)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19248
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
31536Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2782928776041
40112Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6778
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80835Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID137488.1StrainInfo: A central database for resolving microbial strain identifiers
120891Curators of the CIPCollection of Institut Pasteur (CIP 109077)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109077