Strain identifier

BacDive ID: 140850

Type strain: Yes

Species: Paenibacillus baekrokdamisoli

Strain Designation: Back-11

Strain history: <- Jung-Sook Lee, KRIBB

NCBI tax ID(s): 1712516 (species)

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General

@ref: 43659

BacDive-ID: 140850

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

description: Paenibacillus baekrokdamisoli Back-11 is an obligate aerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from Sediment soil of a crater lake, 1950 m above sea level.

NCBI tax id

  • NCBI tax id: 1712516
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Jung-Sook Lee, KRIBB

doi: 10.13145/bacdive140850.20230509.8.1

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 baekrokdamisoli
  • full scientific name: Paenibacillus baekrokdamisoli Lee et al. 2016

@ref: 43659

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus baekrokdamisoli

strain designation: Back-11

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43659positive2.4-3.3 µm0.9-1.5 µmrod-shapedyesperitrichous
67771rod-shapedyesperitrichous
67771positive
69480yes96.52
69480positive100

colony morphology

  • @ref: 43659
  • colony color: creamy white, semi-translucent
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

  • @ref: 43659
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43659positivegrowth10-30
43659positiveoptimum25mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
43659positivegrowth6-9alkaliphile
43659positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43659obligate aerobe
67771aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
43659subterminal endospores in swollen sporangiumendosporeyes
69481yes100
69480yes100

halophily

  • @ref: 43659
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %(w/v)

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4365917128adipate-assimilation
4365927689decanoate-assimilation
4365916899D-mannitol-assimilation
4365925115malate-assimilation
4365929864mannitol-assimilation
43659506227N-acetylglucosamine-assimilation
4365918401phenylacetate-assimilation
4365932032potassium gluconate-assimilation
4365953258sodium citrate-assimilation
4365927613amygdalin-builds acid from
4365918305arbutin-builds acid from
4365917057cellobiose-builds acid from
4365915963ribitol-builds acid from
4365918333D-arabitol-builds acid from
4365928847D-fucose-builds acid from
4365912936D-galactose-builds acid from
4365917716lactose-builds acid from
4365962318D-lyxose-builds acid from
4365916899D-mannitol-builds acid from
4365916988D-ribose-builds acid from
4365917924D-sorbitol-builds acid from
4365916443D-tagatose-builds acid from
4365916813galactitol-builds acid from
4365917113erythritol-builds acid from
4365928066gentiobiose-builds acid from
4365928087glycogen-builds acid from
4365917268myo-inositol-builds acid from
4365915443inulin-builds acid from
4365918403L-arabitol-builds acid from
4365918287L-fucose-builds acid from
4365917266L-sorbose-builds acid from
4365965328L-xylose-builds acid from
4365917306maltose-builds acid from
436596731melezitose-builds acid from
43659320061methyl alpha-D-glucopyranoside-builds acid from
4365943943methyl alpha-D-mannoside-builds acid from
43659506227N-acetylglucosamine-builds acid from
43659potassium 2-dehydro-D-gluconate-builds acid from
43659potassium 5-dehydro-D-gluconate-builds acid from
4365932032potassium gluconate-builds acid from
4365917814salicin-builds acid from
4365928017starch-builds acid from
4365917151xylitol-builds acid from
436595291gelatin-hydrolysis
4365922599arabinose+assimilation
4365917234glucose+assimilation
4365930849L-arabinose+assimilation
4365917306maltose+assimilation
4365937684mannose+assimilation
4365917108D-arabinose+builds acid from
4365915824D-fructose+builds acid from
4365917634D-glucose+builds acid from
4365916024D-mannose+builds acid from
4365965327D-xylose+builds acid from
43659esculin ferric citrate+builds acid from
4365917754glycerol+builds acid from
4365930849L-arabinose+builds acid from
4365962345L-rhamnose+builds acid from
4365928053melibiose+builds acid from
4365974863methyl beta-D-xylopyranoside+builds acid from
4365916634raffinose+builds acid from
4365917992sucrose+builds acid from
4365927082trehalose+builds acid from
4365917234glucose+fermentation
436594853esculin+hydrolysis
4365917632nitrate+reduction
4365932528turanose+/-builds acid from

metabolite production

  • @ref: 43659
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43659cytochrome oxidase+1.9.3.1
43659catalase+1.11.1.6
43659alkaline phosphatase+3.1.3.1
43659esterase (C 4)+
43659esterase Lipase (C 8)+
43659leucine arylamidase+3.4.11.1
43659acid phosphatase+3.1.3.2
43659naphthol-AS-BI-phosphohydrolase+
43659alpha-galactosidase+3.2.1.22
43659beta-galactosidase+3.2.1.23
43659beta-glucosidase+3.2.1.21
43659alpha-glucosidase+/-3.2.1.20
43659lipase (C 14)-
43659valine arylamidase-
43659cystine arylamidase-3.4.11.3
43659trypsin-3.4.21.4
43659alpha-chymotrypsin-3.4.21.1
43659beta-glucuronidase-3.2.1.31
43659N-acetyl-beta-glucosaminidase-3.2.1.52
43659alpha-mannosidase-3.2.1.24
43659alpha-fucosidase-3.2.1.51
43659arginine dihydrolase-3.5.3.6
43659urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43659C10:012.1
    43659C12:06.2
    43659C14:012.8
    43659C15:02.1
    43659C16:019.1
    43659C16:1ω7c1.9
    43659C17:1ω8c1.6
    43659C18:1ω9c18.3
    43659C18:2ω6,9c / anteiso-C18:010.8
    43659Unknown C16:3151.09
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 25
  • incubation time: 3
  • incubation_oxygen: aerobic
  • library/peak naming table: TSBA6.1
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
43659Sediment soil of a crater lake, 1950 m above sea levelBaekrokdam, Hallasan, JejuRepublic of KoreaKORAsia
67771From sediment soil of crater lakeBaekrokdam, Hallasan, JejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_10867.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_5382;97_6496;98_8089;99_10867&stattab=map
  • Last taxonomy: Paenibacillus baekrokdamisoli subclade
  • 16S sequence: LC082229
  • Sequence Identity:
  • Total samples: 1533
  • soil counts: 1278
  • aquatic counts: 79
  • animal counts: 57
  • plant counts: 119

Sequence information

16S sequences

  • @ref: 43659
  • description: 16S rRNA gene sequence
  • accession: LC082229
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus baekrokdamisoli KCTC 33723GCA_003945345completencbi1712516
66792Paenibacillus baekrokdamisoli CECT 8890GCA_014191785scaffoldncbi1712516
66792Paenibacillus baekrokdamisoli strain CECT 88901712516.5wgspatric1712516
66792Paenibacillus baekrokdamisoli strain KCTC 337231712516.3completepatric1712516
66792Paenibacillus baekrokdamisoli CECT 88902824296850draftimg1712516
66792Paenibacillus baekrokdamisoli KCTC 337232850738089completeimg1712516

GC content

@refGC-contentmethod
4365945.3high performance liquid chromatography (HPLC)
6777145.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes86.515yes
flagellatedyes73.645no
gram-positiveyes87.008yes
anaerobicno99.071no
aerobicyes86.965no
halophileno97.227no
spore-formingyes96.1yes
glucose-utilyes91.449yes
thermophileno99.886yes
glucose-fermentno83.544yes

External links

@ref: 43659

culture collection no.: KCTC 33723, CECT 8890

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26868819Paenibacillus baekrokdamisoli sp. nov., isolated from soil of crater lake.Lee KC, Kim KK, Kim JS, Kim DS, Ko SH, Yang SH, Lee JSInt J Syst Evol Microbiol10.1099/ijsem.0.0009682016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lakes/*microbiology, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32293556Paenibacillus solisilvae sp. nov., isolated from birch forest soil.Kong D, Zhang Q, Jiang X, Ma Q, Han X, Zhou Y, Xue H, Zhang Y, Zhang W, Ruan ZInt J Syst Evol Microbiol10.1099/ijsem.0.0040932020Bacterial Typing Techniques, Base Composition, *Betula, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Glycolipids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
43659Keun Chul Lee, Kwang Kyu Kim, Jong-Shik Kim, Dae-Shin Kim, Suk-Hyung Ko, Seung-Hoon Yang, Jung-Sook LeePaenibacillus baekrokdamisoli sp. nov., isolated from soil of crater lake10.1099/ijsem.0.000968IJSEM 66: 1937-1942 201626868819
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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