Strain identifier

BacDive ID: 24138

Type strain: Yes

Species: Secundilactobacillus silagei

Strain Designation: IWT126

Strain history: <- DSM <- M Tohno, National Agriculture and Food Res Org (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan, IWT126

NCBI tax ID(s): 1293415 (species)

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General

@ref: 20998

BacDive-ID: 24138

DSM-Number: 27022

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, rod-shaped

description: Secundilactobacillus silagei IWT126 is a microaerophile, mesophilic, rod-shaped bacterium that was isolated from orchardgrass silage.

NCBI tax id

  • NCBI tax id: 1293415
  • Matching level: species

strain history

@refhistory
20998<- M. Tohno, National Agriculture and Food Res. Org. (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan; IWT126
67770M. Tohno IWT126.
67771<- DSM <- M Tohno, National Agriculture and Food Res Org (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan, IWT126

doi: 10.13145/bacdive24138.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Secundilactobacillus
  • species: Secundilactobacillus silagei
  • full scientific name: Secundilactobacillus silagei (Tohno et al. 2013) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus silagei

@ref: 20998

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Secundilactobacillus

species: Secundilactobacillus silagei

full scientific name: Secundilactobacillus silagei (Tohno et al. 2013) Zheng et al. 2020

strain designation: IWT126

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
67771rod-shapedno
67771positive
69480no93.799
69480positive99.999

Culture and growth conditions

culture medium

  • @ref: 20998
  • name: MRS MEDIUM (DSMZ Medium 11)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/11
  • composition: Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
20998positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
20998microaerophile
67771anaerobe

spore formation

@refspore formationconfidence
67771no
69481no100
69480no99.997

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
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
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

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
20998----+-+---++----------+-----+-+--------------+-+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
20998orchardgrass (Dactylis glomerata L.) silageDactylis glomerataIwate, HachimantaiJapanJPNAsia
67770Orchardgrass silageHachimantai, IwateJapanJPNAsia
67771From orchardgrass, `Dactylis glomerata` L., silageHachimantai, IwateJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_20720.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_750;97_873;98_2977;99_20720&stattab=map
  • Last taxonomy: Secundilactobacillus
  • 16S sequence: LC589213
  • Sequence Identity:
  • Total samples: 1825
  • soil counts: 155
  • aquatic counts: 237
  • animal counts: 1277
  • plant counts: 156

Safety information

risk assessment

  • @ref: 20998
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20998Lactobacillus silagei gene for 16S ribosomal RNA, partial sequenceAB7869101488ena1302250
67770Secundilactobacillus silagei JCM 19001 gene for 16S rRNA, partial sequenceLC5892131502ena1302250

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Secundilactobacillus silagei JCM 19001GCA_001313225contigncbi1302250
66792Lactobacillus silagei JCM 190011302250.3wgspatric1302250
66792Lactobacillus silagei JCM 19001 strain DSM 270221302250.7wgspatric1302250
66792Lactobacillus silagei JCM 19001 strain IWT1261302250.4wgspatric1302250
66792Secundilactobacillus silagei JCM 190012734481937draftimg1302250
67770Secundilactobacillus silagei JCM 19001 IWT126GCA_002217945scaffoldncbi1302250
67771Secundilactobacillus silagei JCM 19001 DSM 27022GCA_004354595contigncbi1302250

GC content

@refGC-contentmethod
2099845.6high performance liquid chromatography (HPLC)
6777144.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.603no
gram-positiveyes96.053yes
anaerobicno85.315no
halophileyes87.065no
spore-formingno94.258yes
thermophileno99.279yes
glucose-utilyes87.342no
aerobicno96.747yes
flagellatedno97.932yes
glucose-fermentyes84.892no

External links

@ref: 20998

culture collection no.: DSM 27022, JCM 19001, KCTC 21050

straininfo link

  • @ref: 88096
  • straininfo: 391583

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23919960Lactobacillus silagei sp. nov., isolated from orchardgrass silage.Tohno M, Kitahara M, Irisawa T, Masuda T, Uegaki R, Ohkuma M, Tajima KInt J Syst Evol Microbiol10.1099/ijs.0.053124-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Dactylis/*microbiology, Fatty Acids/chemistry, Japan, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silage/*microbiologyGenetics
Phylogeny35834933Characterization of two novel pentose-fermenting and GABA-producing species: Levilactobacillus tujiorum sp. nov. and Secundilactobacillus angelensis sp. nov. Isolated from a solid-state fermented zha-chili.Zhang Z, Wang Y, Dong Y, Xiang F, Zhang Y, Zhang H, Sun Y, Guo ZSyst Appl Microbiol10.1016/j.syapm.2022.1263442022Bacterial Typing Techniques, Base Composition, Carbon, *Cardiolipins, Catalase/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Glycolipids, Nucleic Acid Hybridization, *Pentoses, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, gamma-Aminobutyric Acid/geneticsTranscriptome

Reference

@idauthorstitledoi/urlcatalogue
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
20998Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27022Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27022)
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
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
88096Reimer, 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-ID391583.1