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BacDive ID 11588
Type strain
Strain Designation GMP01
Culture col. no. DSM 17253 CECT 5760 LMG 20987 GMP01 CIP 108371
NCBI tax ID(s) 221028
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 10 (current version):
version 10 (current version)

General

@ref: 6854

BacDive-ID: 11588

DSM-Number: 17253

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

description: Paenibacillus favisporus GMP01 is a facultative anaerobe, spore-forming, mesophilic prokaryote that was isolated from faeces of cow.

NCBI tax id

  • NCBI tax id: 221028
  • Matching level: species

strain history

@refhistory
6854<- E. Velázquez Pérez
119294CIP <- 2004, CECT <- E. Velazquez: strain GMP01

doi: 10.13145/bacdive11588.20251217.10

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: kingdom/bacillati
  • keyword: phylum/bacillota
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Paenibacillus
  • species: Paenibacillus favisporus
  • full scientific name: Paenibacillus favisporus Velázquez et al. 2004

@ref: 6854

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus favisporus

full scientific name: Paenibacillus favisporus Velázquez et al. 2004

strain designation: GMP01

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29934variable02-03 µm0.5-0.7 µmrod-shapedyes
119294positiverod-shapedyes

colony morphology

  • @ref: 119294

pigmentation

  • @ref: 29934
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6854CASO 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
32911MEDIUM 595 - for Cellulomonas xylanilyticayesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.500 g);Agar (20.000 g);Yeast extract (10.000 g);Di Potassium monohydrogenophosphate (1.000 g);Xylan (5.000 g)
119294CIP Medium 595yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=595

culture temp

@refgrowthtypetemperature
6854positivegrowth30
29934positiveoptimum37
32911positivegrowth30
119294positivegrowth22-45
119294negativegrowth10
119294negativegrowth55

culture pH

@refabilitytypepH
29934positiveoptimum7
119294positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29934facultative anaerobe
119294facultative anaerobe

spore formation

@refspore formation
29934yes
119294yes

halophily

@refsaltgrowthtested relationconcentration
119294NaClpositivegrowth0-4 %
119294NaClnogrowth6 %
119294NaClnogrowth8 %
119294NaClnogrowth10 %

observation

  • @ref: 29934
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2993417234glucose+carbon source
2993424996lactate+carbon source
2993417306maltose+carbon source
2993429864mannitol+carbon source
2993437684mannose+carbon source
2993428053melibiose+carbon source
2993416634raffinose+carbon source
2993426546rhamnose+carbon source
2993417992sucrose+carbon source
2993418222xylose+carbon source
2993417632nitrate+reduction
11929416947citrate-carbon source
1192944853esculin+hydrolysis
119294606565hippurate-hydrolysis
11929417632nitrate+reduction
11929416301nitrite-reduction
11929417632nitrate+respiration
6837118403L-arabitol-builds acid from
6837124265gluconate-builds acid from
6837118333D-arabitol-builds acid from
6837128087glycogen-builds acid from
6837116634raffinose+builds acid from
6837128017starch+builds acid from
6837117992sucrose+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-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
6837127613amygdalin+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
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

metabolite production

  • @ref: 119294
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11929415688acetoin-
11929417234glucose-

enzymes

@refvalueactivityec
29934catalase+1.11.1.6
29934gelatinase+
29934cytochrome oxidase+1.9.3.1
29934urease+3.5.1.5
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
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
119294oxidase+
119294beta-galactosidase+3.2.1.23
119294alcohol dehydrogenase-1.1.1.1
119294gelatinase-
119294amylase-
119294DNase-
119294caseinase-3.4.21.50
119294catalase+1.11.1.6
119294tween esterase-
119294gamma-glutamyltransferase-2.3.2.2
119294lecithinase-
119294lipase-
119294lysine decarboxylase-4.1.1.18
119294ornithine decarboxylase-4.1.1.17
119294protease-
119294urease+3.5.1.5
68382beta-galactosidase+3.2.1.23

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119294--++-+----++++--+--+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119294---+++--+/-+++/-+/-----+---+/-++/-++++++++/-+/-+/-++--++/----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119294+--+---+-+++---++-+++++------------+-+----------------++----+-------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
6854faeces of cowSpainESPEurope
119294Animal, Cow, faecesSpainESPEuropeSalamanca1984

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5101.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_2482;97_3032;98_3807;99_5101&stattab=map
  • Last taxonomy: Paenibacillus
  • 16S sequence: AY208751
  • Sequence Identity:
  • Total samples: 3736
  • soil counts: 2631
  • aquatic counts: 282
  • animal counts: 403
  • plant counts: 420

Interaction and safety

risk assessment

@refbiosafety levelbiosafety level comment
68541Risk group (German classification)
1192941Risk group (French classification)

Sequence information

Genome sequences

  • @ref: 124043
  • description: ASM4054541v1 assembly for Paenibacillus favisporus DSM 17253
  • assembly level: contig
  • INSDC accession: GCA_040545415
  • IMG accession: 2928311319
  • NCBI tax ID: 221028
  • score: 74.83

16S sequences

  • @ref: 6854
  • description: Paenibacillus favisporus strain GMP01 16S ribosomal RNA gene, partial sequence
  • accession: AY208751
  • length: 1547
  • database: nuccore
  • NCBI tax ID: 221028

GC content

  • @ref: 6854
  • GC-content: 53

Literature

@ref: 6854

culture collection no.: DSM 17253, CECT 5760, LMG 20987, CIP 108371

straininfo link

  • @ref: 126262
  • straininfo: 85131

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14742459Paenibacillus favisporus sp. nov., a xylanolytic bacterium isolated from cow faeces.Velazquez E, de Miguel T, Poza M, Rivas R, Rossello-Mora R, Villa TGInt J Syst Evol Microbiol10.1099/ijs.0.02709-02004Animals, Bacillaceae/classification/genetics/growth & development/*isolation & purification, Cattle/microbiology, Feces/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny15879272Paenibacillus rhizosphaerae sp. nov., isolated from the rhizosphere of Cicer arietinum.Rivas R, Gutierrez C, Abril A, Mateos PF, Martinez-Molina E, Ventosa A, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.63513-02005Aerobiosis, Argentina, Base Composition, Carbohydrate Metabolism, Catalase/analysis, Cicer/*microbiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Esculin/metabolism, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gentian Violet, Gram-Positive Endospore-Forming Rods/*classification/cytology/*isolation & purification/physiology, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phenazines, Phylogeny, Plant Roots/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial, beta-Glucosidase/analysisEnzymology
23408395Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park.Mead DA, Lucas S, Copeland A, Lapidus A, Cheng JF, Bruce DC, Goodwin LA, Pitluck S, Chertkov O, Zhang X, Detter JC, Han CS, Tapia R, Land M, Hauser LJ, Chang YJ, Kyrpides NC, Ivanova NN, Ovchinnikova G, Woyke T, Brumm C, Hochstein R, Schoenfeld T, Brumm P.Stand Genomic Sci10.4056/sigs.26057922012Geobacillus Sp. Y412mc10, Paenibacillus Sp. Y412mc10, Obsidian Hot Spring

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6854Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17253)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17253
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
29934Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2630528776041
32911Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5986
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
119294Curators of the CIPCollection of Institut Pasteur (CIP 108371)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108371
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
126262A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer10.1093/database/baaf059StrainInfo—the central database for linked microbial strain identifiers

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