Strain identifier

BacDive ID: 11514

Type strain: Yes

Species: Paenibacillus chitinolyticus

Strain Designation: EAG-3

Strain history: CIP <- 1996, IFO <- 1994, R. Takata, Cool. Agr. Ehime Univ., Japan: strain EAG3

NCBI tax ID(s): 1220558 (strain), 79263 (species)

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General

@ref: 4163

BacDive-ID: 11514

DSM-Number: 11030

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, motile

description: Paenibacillus chitinolyticus EAG-3 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from forest soil.

NCBI tax id

NCBI tax idMatching level
79263species
1220558strain

strain history

@refhistory
4163<- IFO <- R. Takata, Ehime University, Japan
67770NBRC 15660 <-- IFO 15660 <-- R. Takata EAG-3.
118237CIP <- 1996, IFO <- 1994, R. Takata, Cool. Agr. Ehime Univ., Japan: strain EAG3

doi: 10.13145/bacdive11514.20230509.8.1

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

  • synonyms

    • @ref: 20215
    • synonym: Bacillus chitinolyticus

@ref: 4163

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus chitinolyticus

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

strain designation: EAG-3

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.82
69480100positive
118237nopositiverod-shaped

colony morphology

  • @ref: 118237
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4163NUTRIENT 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 Yeast extract 3.0 g/l Distilled water
39137MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118237CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4163positivegrowth30mesophilic
39137positivegrowth30mesophilic
67770positivegrowth30mesophilic
118237positivegrowth22-37
118237nogrowth10psychrophilic
118237nogrowth45thermophilic
118237nogrowth55thermophilic

culture pH

  • @ref: 118237
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 118237
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100
118237yes

halophily

@refsaltgrowthtested relationconcentration
118237NaClpositivegrowth0-4 %
118237NaClnogrowth6 %
118237NaClnogrowth8 %
118237NaClnogrowth10 %

observation

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

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
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371esculin+builds acid from4853
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-mannoside-builds acid from43943
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
68371methyl beta-D-xylopyranoside-builds acid from74863
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
118237citrate-carbon source16947
118237esculin+hydrolysis4853
118237hippurate+hydrolysis606565
118237nitrate-reduction17632
118237nitrite-reduction16301
118237nitrate-respiration17632

metabolite production

  • @ref: 118237
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11823715688acetoin-
11823717234glucose-

enzymes

@refvalueactivityec
118237oxidase+
118237beta-galactosidase+3.2.1.23
118237alcohol dehydrogenase-1.1.1.1
118237gelatinase-
118237amylase-
118237DNase-
118237caseinase-3.4.21.50
118237catalase+1.11.1.6
118237tween esterase-
118237gamma-glutamyltransferase-2.3.2.2
118237lecithinase-
118237lipase-
118237lysine decarboxylase-4.1.1.18
118237ornithine decarboxylase-4.1.1.17
118237urease-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
118237-+++---------+-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118237----+-----+-+-------+/-++/-+/-++/-++-+++---++-++------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118237+-+++-++++++--++++++--+--------+--++-----------------------++-------------------------+-----++-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4163forest soilKaya, Kagoshima PrefectureJapanJPNAsia
67770Forest soil in KayaKagoshima Pref.JapanJPNAsia
118237Environment, SoilKagoshimaJapanJPNAsia1993

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1072.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_621;97_724;98_843;99_1072&stattab=map
  • Last taxonomy: Paenibacillus chitinolyticus subclade
  • 16S sequence: AB045100
  • Sequence Identity:
  • Total samples: 314
  • soil counts: 119
  • aquatic counts: 47
  • animal counts: 77
  • plant counts: 71

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
41631Risk group (German classification)
1182371Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus chitinolyticus gene for 16S rRNA, partial sequenceAB0451001485ena79263
20218Bacillus chitinolyticus gene for 16S ribosomal RNAAB0211831534ena79263
20218Paenibacillus chitinolyticus gene for 16S rRNA, partial sequence, strain: NBRC 15660AB6809381479ena79263

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus chitinolyticus KCCM 41400GCA_004117095completencbi79263
66792Paenibacillus chitinolyticus NBRC 156601220558.3wgspatric1220558
66792Paenibacillus chitinolyticus strain KCCM 4140079263.3completepatric79263
66792Paenibacillus chitinolyticus KCCM 414002848028059completeimg79263
66792Paenibacillus chitinolyticus NBRC 156602600255075draftimg1220558
67770Paenibacillus chitinolyticus NBRC 15660GCA_000739915contigncbi1220558

GC content

  • @ref: 4163
  • GC-content: 51.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes85.691no
flagellatedyes84.752no
gram-positiveyes74.435no
anaerobicno98.223no
aerobicyes91.921no
halophileno97.927no
spore-formingyes96.139no
thermophileno99.785yes
glucose-utilyes89.006no
glucose-fermentno87.989no

External links

@ref: 4163

culture collection no.: DSM 11030, IFO 15660, NBRC 15660, JCM 12162, CCM 4527, CIP 104914, KCCM 41400, KCTC 3791, LMG 18047, NRRL B-23119, EAG 3

straininfo link

  • @ref: 80746
  • straininfo: 14019

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
Phylogeny16957110Paenibacillus gansuensis sp. nov., isolated from desert soil of Gansu Province in China.Lim JM, Jeon CO, Lee JC, Xu LH, Jiang CL, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.64210-02006Bacteria/genetics/*isolation & purification, Bacterial Physiological Phenomena, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis, *Soil MicrobiologyGenetics
Phylogeny19126735Paenibacillus contaminans sp. nov., isolated from a contaminated laboratory plate.Chou JH, Lee JH, Lin MC, Chang PS, Arun AB, Young CC, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.001495-02009Bacteria, Aerobic/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Culture Media, DNA, Bacterial/analysis, *Equipment Contamination, Genes, rRNA, Genotype, *Laboratories, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Spores, Bacterial/physiologyCultivation
Enzymology32411515Cloning, expression and characterization of a chitinase from Paenibacillus chitinolyticus strain UMBR 0002.Liu C, Shen N, Wu J, Jiang M, Shi S, Wang J, Wei Y, Yang LPeerJ10.7717/peerj.89642020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4163Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11030)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11030
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
39137Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16875
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
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
80746Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14019.1StrainInfo: A central database for resolving microbial strain identifiers
118237Curators of the CIPCollection of Institut Pasteur (CIP 104914)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104914