Strain identifier

BacDive ID: 133092

Type strain: Yes

Species: Paenibacillus eucommiae

Strain Designation: I12B-01101

Strain history: <- Yu-Qin Zhang, Chinese Acad. Med. Sciences & Peking Union Medical College, CPCC 100226 <- X.-M. Fang

NCBI tax ID(s): 1355755 (species)

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General

@ref: 24880

BacDive-ID: 133092

DSM-Number: 26048

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

description: Paenibacillus eucommiae I12B-01101 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from From surface-sterilized stem of the traditional Chinese medicinal herbal plant, `Eucommia ulmoides`.

NCBI tax id

  • NCBI tax id: 1355755
  • Matching level: species

strain history

@refhistory
24880<- Y.-Q. Zhang, Chinese Acad. Med. Sciences & Peking Union Medical College; CPCC 100226 <- X.-M. Fang
67771<- Yu-Qin Zhang, Chinese Acad. Med. Sciences & Peking Union Medical College, CPCC 100226 <- X.-M. Fang

doi: 10.13145/bacdive133092.20230509.8.1

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 eucommiae
  • full scientific name: Paenibacillus eucommiae Fang et al. 2017

@ref: 24880

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus eucommiae

full scientific name: Paenibacillus eucommiae Fang et al. 2017

strain designation: I12B-01101

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
25258positive2.0-4.0 µm0.8-1.0 µmrod-shapedyesperitrichous
67771rod-shapedyes
67771positive
69480positive100
69480yes97.439

colony morphology

  • @ref: 25258
  • colony size: 0.5-1 mm
  • colony color: pale white
  • incubation period: 3 days
  • medium used: tryptic soy agar (TSA)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25258tryptic soy agar (TSA)yes
25258nutritient agar (NA)yes
25258Reasoner's 2A agar (R2A)no
24880CASO 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

culture temp

@refgrowthtypetemperaturerange
25258positivegrowth10-40
25258positiveoptimum28-32mesophilic
24880positivegrowth30mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25258positivegrowth6.0-10.0alkaliphile
25258positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
25258aerobe
67771aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
25258ellipsoidal, at central positionendosporeyes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
25258NaClpositivegrowth0.0-2.0 %(w/v)
25258NaCloptimum0.0-1.0 %(w/v)

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25258645522-hydroxybutyrate-carbon source
2525873706bromosuccinate-carbon source
25258casein-hydrolysis
2525816947citrate-carbon source
2525818333D-arabitol-carbon source
2525816899D-mannitol-carbon source
2525817924D-sorbitol-carbon source
2525816991dna-hydrolysis
2525816865gamma-aminobutyric acid-carbon source
252585291gelatin-hydrolysis
2525870744glycine-proline-carbon source
2525816977L-alanine-carbon source
2525817464L-galactonic acid gamma-lactone-carbon source
2525818183L-pyroglutamic acid-carbon source
2525817895L-tyrosine-hydrolysis
2525851850methyl pyruvate-carbon source
2525835418n-acetylneuraminate-carbon source
25258skimmed milk-fermentation
2525828017starch-hydrolysis
2525853424tween 20-hydrolysis
2525853423tween 40-hydrolysis
2525853426tween 80-hydrolysis
2525816199urea-hydrolysis
25258739183-O-methyl-D-glucose+carbon source
2525827613amygdalin+builds acid from
2525818305arbutin+builds acid from
2525817057cellobiose+builds acid from
2525828847D-fucose+builds acid from
2525817634D-glucose+builds acid from
2525862318D-lyxose+builds acid from
2525815588D-malate+carbon source
2525816443D-tagatose+builds acid from
252584853esculin+hydrolysis
252584853esculin+builds acid from
2525831605ferric citrate+builds acid from
2525815740formate+carbon source
2525828066gentiobiose+builds acid from
2525817234glucose+fermentation
2525832323glucuronamide+carbon source
2525817754glycerol+builds acid from
2525817268myo-inositol+carbon source
2525829991L-aspartate+carbon source
2525818287L-fucose+builds acid from
2525829985L-glutamate+carbon source
2525815971L-histidine+carbon source
2525816651(S)-lactate+carbon source
2525818019L-lysine+builds acid from
2525815589L-malate+carbon source
2525815729L-ornithine+builds acid from
2525862345L-rhamnose+carbon source
2525862345L-rhamnose+builds acid from
2525817115L-serine+carbon source
2525828053melibiose+builds acid from
25258320061methyl alpha-D-glucopyranoside+builds acid from
2525874863methyl beta-D-xylopyranoside+builds acid from
2525863154N-acetyl-beta-D-mannosamine+carbon source
252588006N-acetyl-D-glucosamine+carbon source
2525828037N-acetylgalactosamine+carbon source
25258506227N-acetylglucosamine+builds acid from
2525817632nitrate+reduction
25258potassium 5-dehydro-D-gluconate+builds acid from
2525832032potassium gluconate+builds acid from
2525826490quinate+carbon source
2525816634raffinose+builds acid from
2525817814salicin+builds acid from
2525817164stachyose+carbon source
2525817992sucrose+builds acid from
2525827082trehalose+builds acid from
2525832528turanose+builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
2525815688acetoinno
2525816136hydrogen sulfideno
2525835581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
2525817234glucose+
2525815688acetoin-

enzymes

@refvalueactivityec
25258alpha-galactosidase+3.2.1.22
25258catalase+1.11.1.6
25258cystine arylamidase-3.4.11.3
25258cytochrome oxidase+1.9.3.1
25258esterase Lipase (C 8)+
25258lysine decarboxylase+4.1.1.18
25258naphthol-AS-BI-phosphohydrolase+
25258urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25258C15:0 anteiso51.9
    25258C16:06.5
    25258C15:0 iso22.8
    25258C16:0 iso6.4
  • type of FA analysis: whole cell analysis
  • incubation medium: tryptical soy broth (TSB)
  • agar/liquid: liquid
  • incubation temperature: 28
  • incubation time: 3
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA 6
  • system: MIS MIDI
  • method/protocol: Sasser 1990

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost speciesenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
67771From surface-sterilized stem of the traditional Chinese medicinal herbal plant, `Eucommia ulmoides`Oliver, Dali, Yunnan ProvinceChinaCHNAsia
24880surface-sterilized stem of the traditional Chinese medicinal herbal plant Eucommia ulmoides OliverYunnan Province, DaliChinaCHNAsiaEucommia ulmoides
25258isolation mediumstarch 2 g/l, K2HPO4 0.5 g/l, MgSO4 0.5 g/l, KNO3 1 g/l, NaCl 0.4 g/l, FeSO4x 7H2O 0.01 g/l and agar 15 g/l, pH 7.23 weeks28

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Stem (Branch)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_69380.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_29783;97_37613;98_48765;99_69380&stattab=map
  • Last taxonomy: Paenibacillus eucommiae subclade
  • 16S sequence: KC589216
  • Sequence Identity:
  • Total samples: 6679
  • soil counts: 4896
  • aquatic counts: 269
  • animal counts: 411
  • plant counts: 1103

Safety information

risk assessment

  • @ref: 24880
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24880
  • description: Paenibacillus eucommiae strain I12B-01101 16S ribosomal RNA gene, partial sequence
  • accession: KC589216
  • length: 1432
  • database: ena
  • NCBI tax ID: 1355755

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus eucommiae DSM 26048GCA_017874215contigncbi1355755
66792Paenibacillus eucommiae strain DSM 260481355755.3wgspatric1355755
66792Paenibacillus eucommiae DSM 260482913465876draftimg1355755

GC content

@refGC-contentmethod
2488047.9thermal denaturation, midpoint method (Tm)
6777147.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes90.003yes
gram-positiveyes88.273yes
anaerobicno98.771yes
halophileno92.316no
spore-formingyes94.264yes
thermophileno99.64yes
glucose-utilyes86.574no
flagellatedyes82.951no
aerobicyes87.963yes
glucose-fermentno86.691yes

External links

@ref: 24880

culture collection no.: DSM 26048, KCTC 33054, CPCC 100226, CPCC 100226T

straininfo link

  • @ref: 91357
  • straininfo: 401014

literature

  • topic: Phylogeny
  • Pubmed-ID: 27959785
  • title: Paenibacillus eucommiae sp. nov., isolated from a traditional Chinese medicinal herbal plant, Eucommia ulmoides Oliver.
  • authors: Fang XM, Su J, Wang H, Zhang T, Zhao LL, Liu HY, Ma BP, Zhang YQ, Yu LY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001730
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Eucommiaceae/*microbiology, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plants, Medicinal/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24880Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26048Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26048)
25258X. M. S. Fang, J.,Wang, H.,Zhang, T.,Zhao, L. L.,Liu, H. Y.,Ma, B. P.,Zhang, Y. Q.,Yu, L. Y.Paenibacillus eucommiae sp. nov., isolated from a traditional Chinese medicinal herbal plant, Eucommia ulmoides Oliver10.1099/ijsem.0.001730IJSEM 67: 993-997 201727959785
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91357Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID401014.1