Strain identifier

BacDive ID: 11636

Type strain: Yes

Species: Paenibacillus nanensis

Strain Designation: MX2-3

Strain history: <- S Tanasupawat, Chulalongkorn Univ., Thailand

NCBI tax ID(s): 393251 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 16589

BacDive-ID: 11636

DSM-Number: 22867

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

description: Paenibacillus nanensis MX2-3 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from soil sample.

NCBI tax id

  • NCBI tax id: 393251
  • Matching level: species

strain history

@refhistory
16589<- KCTC
67771<- S Tanasupawat, Chulalongkorn Univ., Thailand

doi: 10.13145/bacdive11636.20230509.8.1

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 nanensis
  • full scientific name: Paenibacillus nanensis Khianngam et al. 2009

@ref: 16589

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus nanensis

full scientific name: Paenibacillus nanensis Khianngam et al. 2009

strain designation: MX2-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
28883positive3-8 µm1-1.2 µmrod-shapedyes
67771rod-shapedyesperitrichous
67771positive
69480yes97.517
69480positive100

pigmentation

  • @ref: 28883
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16589
  • name: XYLAN MEDIUM (DSMZ Medium 1235)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1235
  • composition: Name: XYLAN MEDIUM (DSMZ Medium 1235; with strain-specific modifications) Composition: Agar 15.0 g/l Xylan 10.0 g/l Peptone 5.0 g/l K2HPO4 4.0 g/l Yeast extract 1.0 g/l MgSO4 x 7 H2O 1.0 g/l KCl 0.2 g/l FeSO4 x 7 H2O 0.02 g/l MnSO4 Distilled water

culture temp

@refgrowthtypetemperaturerange
16589positivegrowth30mesophilic
28883positivegrowth20-45
28883positiveoptimum37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
28883positivegrowth6.5-9alkaliphile
28883positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
28883facultative anaerobe
67771aerobe

spore formation

@refspore formationtype of sporeconfidence
28883yes
67771yesendospore
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
28883NaClpositivegrowth0-3 %
28883NaClpositiveoptimum1.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2888315963ribitol+carbon source
2888322599arabinose+carbon source
2888318403L-arabitol+carbon source
2888317057cellobiose+carbon source
2888328757fructose+carbon source
2888333984fucose+carbon source
2888328260galactose+carbon source
2888324265gluconate+carbon source
2888317234glucose+carbon source
2888317754glycerol+carbon source
2888328087glycogen+carbon source
2888317716lactose+carbon source
2888328053melibiose+carbon source
2888316634raffinose+carbon source
2888333942ribose+carbon source
2888317814salicin+carbon source
2888330911sorbitol+carbon source
2888317151xylitol+carbon source
2888318222xylose+carbon source
288834853esculin+hydrolysis
2888317632nitrate+reduction

enzymes

@refvalueactivityec
28883catalase+1.11.1.6
28883cytochrome oxidase+1.9.3.1
28883urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16589soil sampleNan province, Muang districtThailandTHAAsia
67771From soilThailandTHAAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_113068.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_7772;97_20209;98_76614;99_113068&stattab=map
  • Last taxonomy: Paenibacillus nanensis subclade
  • 16S sequence: AB265206
  • Sequence Identity:
  • Total samples: 16
  • soil counts: 10
  • animal counts: 6

Safety information

risk assessment

  • @ref: 16589
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16589
  • description: Paenibacillus nanensis gene for 16S rRNA, partial sequence
  • accession: AB265206
  • length: 1460
  • database: ena
  • NCBI tax ID: 393251

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus nanensis DSM 22867GCA_003583765contigncbi393251
66792Paenibacillus nanensis strain DSM 22867393251.3wgspatric393251

GC content

  • @ref: 16589
  • GC-content: 52.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes90.171no
anaerobicno98.878yes
halophileno91.682no
spore-formingyes95.648yes
glucose-utilyes89.443yes
aerobicyes90.292no
motileyes91.964yes
flagellatedyes89.714yes
thermophileno99.276yes
glucose-fermentno88.917no

External links

@ref: 16589

culture collection no.: DSM 22867, KCTC 13044, PCU 276, TISTR 1828

straininfo link

  • @ref: 80861
  • straininfo: 397028

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19244442Paenibacillus thailandensis sp. nov. and Paenibacillus nanensis sp. nov., xylanase-producing bacteria isolated from soil.Khianngam S, Akaracharanya A, Tanasupawat S, Lee KC, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.000406-02009Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis/isolation & purification, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Gram-Positive Endospore-Forming Rods/*classification/*enzymology/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/physiology, Thailand, Xylosidases/*biosynthesisEnzymology
Phylogeny19946060Paenibacillus sputi sp. nov., isolated from the sputum of a patient with pulmonary disease.Kim KK, Lee KC, Yu H, Ryoo S, Park Y, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.017137-02009Aerobiosis, Anaerobiosis, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Gram-Positive Bacterial Infections/*microbiology, Humans, Lung Diseases/*microbiology, Molecular Sequence Data, Paenibacillus/*classification/*isolation & purification, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/cytology, Sputum/*microbiologyPathogenicity
Phylogeny29458465Xylanibacillus composti gen. nov., sp. nov., isolated from compost.Kukolya J, Bata-Vidacs I, Luzics S, Toth E, Keki Z, Schumann P, Tancsics A, Nagy I, Olasz F, Toth AInt J Syst Evol Microbiol10.1099/ijsem.0.0025232018Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, *Composting, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16589Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22867)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22867
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
28883Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2532328776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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.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
80861Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397028.1StrainInfo: A central database for resolving microbial strain identifiers