Strain identifier

BacDive ID: 11607

Type strain: Yes

Species: Paenibacillus elgii

Strain Designation: LGC-32714SD17, SD17

Strain history: CIP <- 2004, NBRC <- Korea Res. Inst. Biosci. Biotec., K.S. Bae: strain SD17

NCBI tax ID(s): 1349776 (strain), 189691 (species)

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General

@ref: 16236

BacDive-ID: 11607

DSM-Number: 22254

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

description: Paenibacillus elgii LGC-32714SD17 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from roots of Perilla frutescens.

NCBI tax id

NCBI tax idMatching level
1349776strain
189691species

strain history

@refhistory
16236<- M. Miyashita, Natl. Inst. of Technol. and Evaluation (NITE), Japan <- D.-S. Kim; SD17
119007CIP <- 2004, NBRC <- Korea Res. Inst. Biosci. Biotec., K.S. Bae: strain SD17

doi: 10.13145/bacdive11607.20230509.8.1

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 elgii
  • full scientific name: Paenibacillus elgii Kim et al. 2004

@ref: 16236

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus elgii

full scientific name: Paenibacillus elgii Kim et al. 2004

strain designation: LGC-32714SD17, SD17

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29886variable4 µm0.9 µmrod-shapedyes
69480yes94.437
69480positive100
119007positiverod-shapedyes

colony morphology

  • @ref: 119007
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16236NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l MnSO4 0.01 g/l Distilled water
16236CASO 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
33202MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
36889MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119007CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16236positivegrowth30mesophilic
29886positivegrowth20-45
29886positiveoptimum32.5mesophilic
33202positivegrowth30mesophilic
36889positivegrowth30mesophilic
119007positivegrowth22-55
119007nogrowth10psychrophilic

culture pH

@refabilitytypepHPH range
29886positivegrowth6-8.5alkaliphile
29886positiveoptimum7
119007positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29886facultative anaerobe
119007facultative anaerobe

spore formation

@refspore formationconfidence
29886yes
69481yes100
69480yes100
119007yes

halophily

@refsaltgrowthtested relationconcentration
29886NaClpositivegrowth0-2 %
29886NaClpositiveoptimum1 %
119007NaClpositivegrowth0-2 %
119007NaClnogrowth4 %
119007NaClnogrowth6 %
119007NaClnogrowth8 %
119007NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2988617234glucose+carbon source
2988617754glycerol+carbon source
2988633942ribose+carbon source
2988653423tween 40+carbon source
2988618222xylose+carbon source
298864853esculin+hydrolysis
2988617632nitrate+reduction
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
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
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
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
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
1190074853esculin+hydrolysis
119007606565hippurate+hydrolysis
11900717632nitrate+reduction
11900716301nitrite-reduction
11900717632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
2988635581indoleyes
11900735581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
2988635581indole+
11900715688acetoin-
11900717234glucose-

enzymes

@refvalueactivityec
29886catalase+1.11.1.6
119007oxidase-
119007beta-galactosidase+3.2.1.23
119007alcohol dehydrogenase-1.1.1.1
119007gelatinase+
119007amylase+
119007DNase+
119007caseinase+3.4.21.50
119007catalase+1.11.1.6
119007tween esterase+
119007gamma-glutamyltransferase-2.3.2.2
119007lecithinase+
119007lipase+
119007lysine decarboxylase-4.1.1.18
119007ornithine decarboxylase-4.1.1.17
119007protease+
119007urease-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
119007-+++++----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119007+-+/--++---++++---++++++++++++++++--++++++---+/---+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119007+++++-++++++-+-+-+-+-++---+----++++++----+------++---------++--------------+--+++----+--+++-+++--+-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
16236roots of Perilla frutescensPerilla frutescensSeocheon CountyRepublic of KoreaKORAsia
119007Plant, Roots of Perilla frutescensSeocheon CountyRepublic of KoreaKORAsia1999

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7139.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_3348;97_4106;98_5253;99_7139&stattab=map
  • Last taxonomy: Paenibacillus
  • 16S sequence: AY090110
  • Sequence Identity:
  • Total samples: 404
  • soil counts: 257
  • aquatic counts: 35
  • animal counts: 97
  • plant counts: 15

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
162361Risk group (German classification)
1190071Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paenibacillus elgii gene for 16S rRNA, partial sequence, strain: NBRC 100335AB6811511459ena189691
16236Paenibacillus elgii strain SD17 16S ribosomal RNA gene, partial sequenceAY0901101471ena189691

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus elgii NBRC 100335GCA_004000865contigncbi1349776
66792Paenibacillus elgii NBRC 1003351349776.3wgspatric1349776
66792Paenibacillus elgii NBRC 1003352839866320draftimg1349776

GC content

  • @ref: 16236
  • GC-content: 51.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes88.341yes
gram-positiveno59.462yes
anaerobicno98.288no
halophileno95.662no
spore-formingyes92.169yes
glucose-utilyes90.957yes
flagellatedyes76.552no
thermophileno98.779yes
aerobicyes81.243no
glucose-fermentno87.626no

External links

@ref: 16236

culture collection no.: DSM 22254, CIP 108552, KCTC 10016BP, NBRC 100335, CIP 108599

straininfo link

  • @ref: 80833
  • straininfo: 134440

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545429Paenibacillus elgii sp. nov., with broad antimicrobial activity.Kim DS, Bae CY, Jeon JJ, Chun SJ, Oh HW, Hong SG, Baek KS, Moon EY, Bae KSInt J Syst Evol Microbiol10.1099/ijs.0.02414-02004Anaerobiosis, Anti-Bacterial Agents/*biosynthesis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gram-Positive Endospore-Forming Bacteria/*classification/cytology/isolation & purification/physiology, Molecular Sequence Data, Perilla frutescens/*microbiology, Phylogeny, Plant Roots/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TemperatureEnzymology
Phylogeny20543152Paenibacillus tianmuensis sp. nov., isolated from soil.Wu X, Fang H, Qian C, Wen Y, Shen X, Li O, Gao HInt J Syst Evol Microbiol10.1099/ijs.0.024109-02010China, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16236Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22254)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22254
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
29886Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126259
33202Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6187
36889Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6246
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
80833Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134440.1StrainInfo: A central database for resolving microbial strain identifiers
119007Curators of the CIPCollection of Institut Pasteur (CIP 108599)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108599