Strain identifier

BacDive ID: 140352

Type strain: Yes

Species: Neobacillus notoginsengisoli

Strain Designation: SYP-B691

Strain history: Y.-X. Zhang; Shenyang Pharm. Univ., China; SYP-B691.

NCBI tax ID(s): 1578198 (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 8.1 (current version)

General

@ref: 42959

BacDive-ID: 140352

DSM-Number: 29196

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

description: Neobacillus notoginsengisoli SYP-B691 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from soil, rhizosphere of Panax notoginseng.

NCBI tax id

  • NCBI tax id: 1578198
  • Matching level: species

strain history

@refhistory
42959<- Y. Zhang, Shenyang Pharmaceutical Univ., China; SYP-B691 <- M. Zhang and Y. Zhang
67770Y.-X. Zhang; Shenyang Pharm. Univ., China; SYP-B691.

doi: 10.13145/bacdive140352.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Neobacillus
  • species: Neobacillus notoginsengisoli
  • full scientific name: Neobacillus notoginsengisoli (Zhang et al. 2017) Patel and Gupta 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus notoginsengisoli

@ref: 42959

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Neobacillus

species: Neobacillus notoginsengisoli

full scientific name: Neobacillus notoginsengisoli (Zhang et al. 2017) Patel and Gupta 2020

strain designation: SYP-B691

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43449positive1.1-5.9 µm0.4-0.7 µmrod-shapedyesperitrichous
69480yes94.828
69480positive99.999

Culture and growth conditions

culture medium

  • @ref: 42959
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43449positivegrowth21-42
43449positiveoptimum37mesophilic
42959positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43449positivegrowth5-10alkaliphile
43449positiveoptimum7-9

Physiology and metabolism

oxygen tolerance

  • @ref: 43449
  • oxygen tolerance: aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
43449ellipsoidal, located sub-terminally and centrally in swollen sporangiaendosporeyes
69481yes100
69480yes99.447

halophily

@refsaltgrowthtested relationconcentration
43449NaClpositivegrowth0-3 %(w/v)
43449NaClpositiveoptimum0-2 %(w/v)

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43449645522-hydroxybutyrate-assimilation
43449309162-oxoglutarate-assimilation
43449739183-O-methyl-D-glucose-assimilation
4344913705acetoacetate-assimilation
4344917057cellobiose-assimilation
4344916947citrate-assimilation
4344918333D-arabitol-assimilation
4344929990D-aspartate-assimilation
4344928847D-fucose-assimilation
4344918024D-galacturonic acid-assimilation
4344916899D-mannitol-assimilation
4344916024D-mannose-assimilation
4344917924D-sorbitol-assimilation
4344923652dextrin-assimilation
4344915740formate-assimilation
4344916537galactarate-assimilation
4344916865gamma-aminobutyric acid-assimilation
4344928066gentiobiose-assimilation
4344916467L-arginine-assimilation
4344918287L-fucose-assimilation
4344915971L-histidine-assimilation
4344918183L-pyroglutamic acid-assimilation
4344962345L-rhamnose-assimilation
4344917716lactose-assimilation
4344925115malate-assimilation
4344928053melibiose-assimilation
4344917268myo-inositol-assimilation
4344928037N-acetylgalactosamine-assimilation
4344917309pectin-assimilation
4344917272propionate-assimilation
4344926490quinate-assimilation
4344916634raffinose-assimilation
4344917814salicin-assimilation
4344917164stachyose-assimilation
4344917992sucrose-assimilation
4344932528turanose-assimilation
4344917234glucose-fermentation
43449casein-hydrolysis
4344962968cellulose-hydrolysis
434495291gelatin-hydrolysis
4344928017starch-hydrolysis
4344953424tween 20-hydrolysis
4344953426tween 80-hydrolysis
4344917925alpha-D-glucose+assimilation
4344978697D-fructose 6-phosphate+assimilation
434498391D-gluconate+assimilation
434495291gelatin+assimilation
4344924265gluconate+assimilation
4344970744glycine-proline+assimilation
4344930849L-arabinose+assimilation
4344924996lactate+assimilation
4344917306maltose+assimilation
43449506227N-acetylglucosamine+assimilation
4344927082trehalose+assimilation
434494853esculin+hydrolysis
4344953423tween 40+hydrolysis
4344953425tween 60+hydrolysis
4344917632nitrate+reduction

metabolite production

@refChebi-IDmetaboliteproduction
4344915688acetoinno
4344916136hydrogen sulfideno
4344935581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4344917234glucose-
4344915688acetoin-

enzymes

@refvalueactivityec
43449catalase+1.11.1.6
43449urease+3.5.1.5
43449arginine dihydrolase-3.5.3.6
43449acid phosphatase+3.1.3.2
43449alkaline phosphatase+3.1.3.1
43449cystine arylamidase+3.4.11.3
43449leucine arylamidase+3.4.11.1
43449trypsin+3.4.21.4
43449valine arylamidase+
43449cytochrome oxidase-1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
42959soil, rhizosphere of Panax notoginsengPanax notoginsengYunnan Province (23° 48' 3.64'' N, 103° 37' 50.04'' E)ChinaCHNAsia23.801103.631
43449rhizospheric soil of Panax notoginsengYunnan Province, PR ChinaChinaCHNAsia23.801103.631
67770Rhizospheric soil of Panax notoginsengPanax notoginsengYunnan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

  • @ref: 42959
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42959
  • description: Bacillus notoginsengisoli strain SYP-B691 16S ribosomal RNA gene, partial sequence
  • accession: KP076294
  • length: 1530
  • database: ena
  • NCBI tax ID: 1578198

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus notoginsengisoli strain JCM 307431578198.3wgspatric1578198
67770Neobacillus notoginsengisoli JCM 30743GCA_003515685contigncbi1578198

GC content

  • @ref: 42959
  • GC-content: 45.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes87.099yes
gram-positiveyes87.437yes
anaerobicno98.448yes
aerobicyes87.794yes
halophileno55.46no
spore-formingyes82.891no
glucose-utilyes87.54yes
flagellatedyes88.302yes
thermophileno98.449no
glucose-fermentno90.777yes

External links

@ref: 42959

culture collection no.: DSM 29196, JCM 30743

straininfo link

  • @ref: 96650
  • straininfo: 405070

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28786779Bacillus notoginsengisoli sp. nov., a novel bacterium isolated from the rhizosphere of Panax notoginseng.Zhang MY, Cheng J, Cai Y, Zhang TY, Wu YY, Manikprabhu D, Li WJ, Zhang YXInt J Syst Evol Microbiol10.1099/ijsem.0.0019752017Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Panax notoginseng/*microbiology, Peptidoglycan/chemistry, Phosphatidylglycerols/analysis, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31364965Two novel species of the family Bacillaceae: Oceanobacillus piezotolerans sp. nov. and Bacillus piezotolerans sp. nov., from deep-sea sediment samples of Yap Trench.Yu L, Tang X, Wei S, Qiu Y, Xu X, Xu G, Wang Q, Yang QInt J Syst Evol Microbiol10.1099/ijsem.0.0035592019Bacillaceae/*classification/isolation & purification, Bacillus/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Pacific Ocean, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryEnzymology

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
42959Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29196Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29196)
43449Meng-Yue Zhang, Juan Cheng, Ying Cai, Tian-Yuan Zhang, Ying-Ying Wu, Deene Manikprabhu, Wen-Jun Li, Yi-Xuan ZhangBacillus notoginsengisoli sp. nov., a novel bacterium isolated from the rhizosphere of Panax notoginseng10.1099/ijsem.0.001975IJSEM 67: 2581-2585 201728786779
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/
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
96650Reimer, 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-ID405070.1