Strain identifier

BacDive ID: 11513

Type strain: Yes

Species: Paenibacillus ehimensis

Strain Designation: EAG-5, EGA 5

Strain history: CIP <- 1996, IFO <- T. Takata, Coll. Agr. Ehime Univ., Japan: strain EGA 5

NCBI tax ID(s): 1220562 (strain), 79264 (species)

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General

@ref: 4162

BacDive-ID: 11513

DSM-Number: 11029

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

description: Paenibacillus ehimensis EAG-5 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from garden soil.

NCBI tax id

NCBI tax idMatching level
1220562strain
79264species

strain history

@refhistory
4162<- IFO <- R. Takata, Ehime University, Japan
67770NBRC 15659 <-- IFO 15659 <-- R. Takata EAG-5.
119000CIP <- 1996, IFO <- T. Takata, Coll. Agr. Ehime Univ., Japan: strain EGA 5

doi: 10.13145/bacdive11513.20250331.9.3

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 ehimensis
  • full scientific name: Paenibacillus ehimensis (Kuroshima et al. 1996) Lee et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Bacillus ehimensis

@ref: 4162

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus ehimensis

full scientific name: Paenibacillus ehimensis (Kuroshima et al. 1996) Lee et al. 2004

strain designation: EAG-5, EGA 5

type strain: yes

Morphology

cell morphology

  • @ref: 119000
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 119000
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4162NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Soil extract 500.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
38522MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119000CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
4162positivegrowth30
38522positivegrowth30
67770positivegrowth30
119000positivegrowth22-37
119000nogrowth10
119000nogrowth45
119000nogrowth55

culture pH

  • @ref: 119000
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 119000
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
119000yes
125438yes91.279
125439yes92.6

halophily

@refsaltgrowthtested relationconcentration
119000NaClpositivegrowth0-2 %
119000NaClnogrowth4 %
119000NaClnogrowth6 %
119000NaClnogrowth8 %
119000NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11900016947citrate-carbon source
1190004853esculin+hydrolysis
119000606565hippurate+hydrolysis
11900017632nitrate+reduction
11900016301nitrite-reduction
11900017632nitrate+respiration
68371Potassium 5-ketogluconate-builds acid from
6837117306maltose+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371Potassium 2-ketogluconate-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
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
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from

metabolite production

  • @ref: 119000
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11900015688acetoin-
11900017234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382lipase (C 14)+
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
119000oxidase+
119000beta-galactosidase+3.2.1.23
119000alcohol dehydrogenase-1.1.1.1
119000gelatinase+
119000DNase-
119000caseinase-3.4.21.50
119000catalase+1.11.1.6
119000tween esterase-
119000gamma-glutamyltransferase-2.3.2.2
119000lecithinase+
119000lipase-
119000lysine decarboxylase-4.1.1.18
119000ornithine decarboxylase-4.1.1.17
119000urease-3.5.1.5
68382leucine arylamidase-3.4.11.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119000-++++------+++------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119000+/---+/-++---++++-------+/-++/-+/-+/-+/-+/-++/-+++--+++-++------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119000+++++-+++++++++++++++++-+++----++++++----+------++---------++--------------+---++---+---++++++--++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4162garden soilMatsuyama, Ehime PrefectureJapanJPNAsia
67770Garden soil in MatsuyamaEhime Pref.JapanJPNAsia
119000Environment, SoilMatsuyamaJapanJPNAsia1993

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
41621Risk group (German classification)
1190001Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus ehimensis gene for 16S ribosomal RNAAB0211841513nuccore79264
20218Bacillus ehimensis strain KCTC3748 16S ribosomal RNA gene, partial sequenceAY1166651452nuccore79264
20218Paenibacillus ehimensis gene for 16S rRNA, partial sequence, strain: NBRC 15659AB6809371487nuccore79264

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus ehimensis NBRC 156591220562.3wgspatric1220562
67770Paenibacillus ehimensis NBRC 15659GCA_004000785contigncbi1220562

GC content

  • @ref: 4162
  • GC-content: 54.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno51.537no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.295yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes91.279no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes63.467no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.075yes
125438motile2+flagellatedAbility to perform flagellated movementyes80.146no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes92.6
125439BacteriaNetmotilityAbility to perform movementyes88.6
125439BacteriaNetgram_stainReaction to gram-stainingvariable88.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe83.9

External links

@ref: 4162

culture collection no.: DSM 11029, IFO 15659, NBRC 15659, JCM 12161, CCM 4526, CIP 104913, KCTC 3748, LMG 18048, NRRL B-23118

straininfo link

  • @ref: 80745
  • straininfo: 10546

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143044Transfer of Bacillus ehimensis and Bacillus chitinolyticus to the genus Paenibacillus with emended descriptions of Paenibacillus ehimensis comb. nov. and Paenibacillus chitinolyticus comb. nov.Lee JS, Pyun YR, Bae KSInt J Syst Evol Microbiol10.1099/ijs.0.02765-02004Bacillus/*classification/genetics/metabolism, Bacteria/*classification/genetics/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species SpecificityMetabolism
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
Enzymology16232486Purification and gene cloning of a chitosanase from Bacillus ehimensis EAG1.Akiyama K, Fujita T, Kuroshima K, Sakane T, Yokota A, Takata RJ Biosci Bioeng10.1016/s1389-1723(99)80050-41999
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/urltitlejournalpubmed
4162Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11029)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11029
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
38522Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16874
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
80745Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10546.1StrainInfo: A central database for resolving microbial strain identifiers
119000Curators of the CIPCollection of Institut Pasteur (CIP 104913)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104913
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1