Strain identifier

BacDive ID: 11551

Type strain: No

Species: Paenibacillus polymyxa

Strain Designation: B.3, B3

Strain history: CIP <- 2001, CECT <- 1999, A. Ramos-Cormenzana, strain: B3

NCBI tax ID(s): 114136 (species)

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General

@ref: 5172

BacDive-ID: 11551

DSM-Number: 13815

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

description: Paenibacillus polymyxa B.3 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from alpechin.

NCBI tax id

  • NCBI tax id: 114136
  • Matching level: species

strain history

@refhistory
5172<- DSMZ <- A. Ramos; B.3
120307CIP <- 2001, CECT <- 1999, A. Ramos-Cormenzana, strain: B3

doi: 10.13145/bacdive11551.20240510.9

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 polymyxa
  • full scientific name: Paenibacillus polymyxa (Prazmowski 1880) Ash et al. 1994

  • synonyms

    @refsynonym
    20215Aerobacillus polymyxa
    20215Clostridium polymyxa
    20215Bacillus polymyxa
    20215Paenibacillus jamilae

@ref: 5172

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus polymyxa

full scientific name: Paenibacillus polymyxa (Prazmowski 1880) Ash et al. 1994

strain designation: B.3, B3

type strain: no

Morphology

cell morphology

  • @ref: 120307
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 120307
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5172CASO 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
33736MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120307CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
5172positivegrowth30
33736positivegrowth30
120307positivegrowth22-45
120307nogrowth10
120307nogrowth55

culture pH

  • @ref: 120307
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 120307
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
120307NaClpositivegrowth0-4 %
120307NaClnogrowth6 %
120307NaClnogrowth8 %
120307NaClnogrowth10 %

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
68371turanose+builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside+builds acid from320061
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
120307citrate-carbon source16947
120307esculin+hydrolysis4853
120307hippurate+hydrolysis606565
120307nitrate+reduction17632
120307nitrite-reduction16301
120307nitrate+respiration17632

metabolite production

  • @ref: 120307
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 120307
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
120307oxidase-
120307beta-galactosidase+3.2.1.23
120307alcohol dehydrogenase-1.1.1.1
120307gelatinase-
120307amylase+
120307DNase-
120307caseinase+3.4.21.50
120307catalase+1.11.1.6
120307tween esterase+
120307gamma-glutamyltransferase-2.3.2.2
120307lecithinase-
120307lipase-
120307lysine decarboxylase-4.1.1.18
120307ornithine decarboxylase-4.1.1.17
120307urease-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
120307--++--------++--+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120307+--+++--+/-++++----+-+/-+-+++++++++++/--+++-++---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120307+++++-+-+----+----++++++-+-----+-+++-----+-------+-----+----+-+--+--------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5172alpechinSpainESPEurope
120307Environment, Olive-mill wastewaterSpainESPEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Industrial wastewater

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
51721Risk group (German classification)
1203071Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5172
  • description: Paenibacillus jamilae partial 16S rRNA gene, strain CECT 5266
  • accession: AJ271157
  • length: 1538
  • database: nuccore
  • NCBI tax ID: 114136

External links

@ref: 5172

culture collection no.: DSM 13815, CECT 5266, CIP 107276

straininfo link

  • @ref: 80779
  • straininfo: 87830

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11594596Paenibacillus jamilae sp. nov., an exopolysaccharide-producing bacterium able to grow in olive-mill wastewater.Aguilera M, Monteoliva-Sanchez M, Suarez A, Guerra V, Lizama C, Bennasar A, Ramos-Cormenzana AInt J Syst Evol Microbiol10.1099/00207713-51-5-16872001Bacillus/classification, Base Composition, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis, Endospore-Forming Bacteria/*classification/*growth & development/physiology, *Industrial Waste, Molecular Sequence Data, Olive Oil, Phylogeny, *Plant Oils, Polysaccharides, Bacterial/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water MicrobiologyGenetics
Phylogeny18319465Paenibacillus woosongensis sp. nov., a xylanolytic bacterium isolated from forest soil.Lee JC, Yoon KHInt J Syst Evol Microbiol10.1099/ijs.0.65350-02008Bacteria/*classification/genetics/isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, *Trees, Xylans/*metabolismMetabolism
Phylogeny23912443Paenibacillus beijingensis sp. nov., a nitrogen-fixing species isolated from wheat rhizosphere soil.Wang LY, Li J, Li QX, Chen SFAntonie Van Leeuwenhoek10.1007/s10482-013-9974-52013Aerobiosis, Bacterial Typing Techniques, Base Composition, Carbon/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Locomotion, Molecular Sequence Data, Nitrogen/metabolism, Nucleic Acid Hybridization, Oxidoreductases, Paenibacillus/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, Soil Microbiology, Triticum/microbiologyMetabolism
Phylogeny31961287Paenibacillus ottowii sp. nov. isolated from a fermentation system processing bovine manure.Velazquez LF, Rajbanshi S, Guan S, Hinchee M, Welsh AInt J Syst Evol Microbiol10.1099/ijsem.0.0036722020Animals, Bacterial Typing Techniques, Base Composition, Cattle, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Fermentation, Manure/*microbiology, Nucleic Acid Hybridization, Paenibacillus/*classification/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TexasTranscriptome
Phylogeny32375953Genome-based reclassification of Paenibacillus jamilae Aguilera et al. 2001 as a later heterotypic synonym of Paenibacillus polymyxa (Prazmowski 1880) Ash et al. 1994.Kwak MJ, Choi SB, Ha SM, Kim EH, Kim BY, Chun JInt J Syst Evol Microbiol10.1099/ijsem.0.0041402020Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Genomics, Nucleic Acid Hybridization, Paenibacillus/*classification, Paenibacillus polymyxa/*classification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Stress32387845Heavy metals-resistant bacteria (HM-RB): Potential bioremediators of heavy metals-stressed Spinacia oleracea plant.Desoky EM, Merwad AM, Semida WM, Ibrahim SA, El-Saadony MT, Rady MMEcotoxicol Environ Saf10.1016/j.ecoenv.2020.1106852020Agriculture, Antioxidants, Ascorbic Acid, Bacillus/physiology, *Biodegradation, Environmental, Cadmium, Chlorophyll, Glutathione, Metals, Heavy/*analysis, Paenibacillus/physiology, Photosynthesis, Plant Leaves/chemistry, Soil, Soil Pollutants/analysis/*toxicity, Spinacia oleracea/microbiology/*physiology
Biotechnology36457524Integrative application of heavy metal-resistant bacteria, moringa extracts, and nano-silicon improves spinach yield and declines its contaminant contents on a heavy metal-contaminated soil.Eltahawy AMAE, Awad EAM, Ibrahim AH, Merwad AMA, Desoky EMFront Plant Sci10.3389/fpls.2022.10190142022

Reference

@idauthorscataloguedoi/urltitle
5172Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13815)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13815
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
33736Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4693
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
80779Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87830.1StrainInfo: A central database for resolving microbial strain identifiers
120307Curators of the CIPCollection of Institut Pasteur (CIP 107276)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107276