Strain identifier

BacDive ID: 132640

Type strain: Yes

Species: Paenibacillus silagei

Strain Designation: LOOC204

Strain history: M. Tohno; NARO Inst. of Livestock & Grassland Sci., Japan; LOOC204.

NCBI tax ID(s): 1670801 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.1 (current version):
version 9:
version 8.1:
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 9.1 (current version)

General

@ref: 24429

BacDive-ID: 132640

DSM-Number: 101953

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, Gram-negative, rod-shaped, colony-forming

description: Paenibacillus silagei LOOC204 is a facultative anaerobe, spore-forming, Gram-negative bacterium that forms circular colonies and was isolated from corn silage stored for three months in a tower silo.

NCBI tax id

  • NCBI tax id: 1670801
  • Matching level: species

strain history

@refhistory
24429<- M. Tohno, National Agriculture and Food Res. Org. (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan; LOOC204
67770M. Tohno; NARO Inst. of Livestock & Grassland Sci., Japan; LOOC204.

doi: 10.13145/bacdive132640.20240916.9.1

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 silagei
  • full scientific name: Paenibacillus silagei Tohno et al. 2016

@ref: 24429

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus silagei

full scientific name: Paenibacillus silagei Tohno et al. 2016

strain designation: LOOC204

type strain: yes

Morphology

cell morphology

  • @ref: 24922
  • gram stain: negative
  • cell length: 3.0-10.0 µm
  • cell width: 0.7-0.9 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 24922
  • colony color: white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: TSA plates

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24922TSA platesyes
24429CASO 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

@refgrowthtypetemperature
24922positivegrowth4.0-37.0
24429positivegrowth30
67770positivegrowth28

culture pH

  • @ref: 24922
  • ability: positive
  • type: growth
  • pH: 6.0-8.5
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 24922
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
24922ellipsoidal,sub-terminal,in swollen sporangiasporeyes
69480yes92.869
69481yes100

halophily

  • @ref: 24922
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 2 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
24922168082-dehydro-D-gluconate-builds acid from
24922581435-dehydro-D-gluconate-builds acid from
2492215963ribitol-builds acid from
2492217108D-arabinose-builds acid from
2492218333D-arabitol-builds acid from
2492228847D-fucose-builds acid from
2492262318D-lyxose-builds acid from
249226731melezitose-builds acid from
2492216988D-ribose-builds acid from
2492217924D-sorbitol-builds acid from
2492216443D-tagatose-builds acid from
2492217113erythritol-builds acid from
2492216813galactitol-builds acid from
2492217268myo-inositol-builds acid from
2492218403L-arabitol-builds acid from
2492217266L-sorbose-builds acid from
2492265328L-xylose-builds acid from
2492243943methyl alpha-D-mannoside-builds acid from
2492227613amygdalin+builds acid from
2492218305arbutin+builds acid from
2492217057cellobiose+builds acid from
2492215824D-fructose+builds acid from
2492212936D-galactose+builds acid from
2492217634D-glucose+builds acid from
2492217716lactose+builds acid from
2492217306maltose+builds acid from
2492216899D-mannitol+builds acid from
2492216024D-mannose+builds acid from
2492228053melibiose+builds acid from
2492216634raffinose+builds acid from
2492217992sucrose+builds acid from
2492216551D-trehalose+builds acid from
2492232528turanose+builds acid from
2492265327D-xylose+builds acid from
249224853esculin+builds acid from
2492228066gentiobiose+builds acid from
2492224265gluconate+builds acid from
2492217754glycerol+builds acid from
2492228087glycogen+builds acid from
2492215443inulin+builds acid from
2492230849L-arabinose+builds acid from
2492218287L-fucose+builds acid from
2492262345L-rhamnose+builds acid from
24922320061methyl alpha-D-glucopyranoside+builds acid from
2492274863methyl beta-D-xylopyranoside+builds acid from
24922506227N-acetylglucosamine+builds acid from
2492217814salicin+builds acid from
2492228017starch+builds acid from
2492217151xylitol+builds acid from

metabolite production

  • @ref: 24922
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: no

metabolite tests

  • @ref: 24922
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
24922acid phosphatase+3.1.3.2
24922alkaline phosphatase-3.1.3.1
24922alpha-fucosidase-3.2.1.51
24922alpha-galactosidase+3.2.1.22
24922alpha-glucosidase+3.2.1.20
24922alpha-mannosidase-3.2.1.24
24922beta-galactosidase+3.2.1.23
24922beta-glucosidase+3.2.1.21
24922beta-glucuronidase-3.2.1.31
24922catalase+1.11.1.6
24922chymotrypsin-3.4.4.5
24922cystine arylamidase-3.4.11.3
24922esterase (C 4)+
24922esterase lipase (C 8)+
24922leucine arylamidase-3.4.11.1
24922lipase (C 14)-
24922N-acetyl-beta-glucosaminidase-3.2.1.52
24922naphthol-AS-BI-phosphohydrolase-
24922trypsin-3.4.21.4
24922valine arylamidase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
24429corn silage stored for three months in a tower siloHokkaido (43° 0' 26'' N 141° 24' 41'' E)JapanJPNAsia43.0072141.411
24922corn silage which had been prepared and stored for three months in a tower siloM17 broth (Difco) agar plates14 days4
67770Corn silageHokkaidoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5647.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_335;97_1860;98_4209;99_5647&stattab=map
  • Last taxonomy: Paenibacillus
  • 16S sequence: LC061279
  • Sequence Identity:
  • Total samples: 1496
  • soil counts: 546
  • aquatic counts: 286
  • animal counts: 395
  • plant counts: 269

Safety information

risk assessment

  • @ref: 24429
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24429
  • description: Paenibacillus silagei gene for 16S ribosomal RNA, partial sequence
  • accession: LC061279
  • length: 1483
  • database: nuccore
  • NCBI tax ID: 1670801

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus silagei DSM 101953GCA_017874735contigncbi1670801
66792Paenibacillus silagei strain DSM 1019531670801.3wgspatric1670801
66792Paenibacillus silagei DSM 1019532913566476draftimg1670801

GC content

@refGC-contentmethod
2442952.2high performance liquid chromatography (HPLC)
6777051.5-52.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes61.37yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.063yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes92.869yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no59.96yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.972yes
69480flagellatedmotile2+Ability to perform flagellated movementyes85.171no

External links

@ref: 24429

culture collection no.: DSM 101953, JCM 30974, MAFF 516319

straininfo link

  • @ref: 90953
  • straininfo: 407444

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27380964Paenibacillus silagei sp. nov. isolated from corn silage.Tohno M, Sakamoto M, Ohkuma M, Tajima KInt J Syst Evol Microbiol10.1099/ijsem.0.0012792016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA-Directed RNA Polymerases/genetics, Fatty Acids/chemistry, Japan, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silage/*microbiology, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiologyTranscriptome
Phylogeny34993761Paenibacillus piscarius sp. nov., a novel nitrogen-fixing species isolated from the gut of the armored catfish Parotocinclus maculicauda.da Silva MBF, Lemos EA, Vollu RE, Abreu F, Rosado AS, Seldin LAntonie Van Leeuwenhoek10.1007/s10482-021-01694-52022Animals, *Catfishes, DNA, Bacterial/genetics, Nitrogen, *Paenibacillus/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics

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
24429Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101953Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101953)
24922M. S. Tohno, Mitsuo,Ohkuma, Moriya,Tajima, KiyoshiPaenibacillus silagei sp. nov. isolated from corn silage10.1099/ijsem.0.001279IJSEM 66: 3873-3877 201627380964
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
90953Reimer, 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-ID407444.1