Strain identifier

BacDive ID: 11439

Type strain: Yes

Species: Brevibacillus panacihumi

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 497735 (species)

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General

@ref: 16591

BacDive-ID: 11439

DSM-Number: 22869

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

description: Brevibacillus panacihumi DSM 22869 is an aerobe, spore-forming, mesophilic bacterium that was isolated from surface soil of a ginseng field.

NCBI tax id

  • NCBI tax id: 497735
  • Matching level: species

strain history

@refhistory
16591<- KCTC <- D.-C. Yang; DCY35
67770D.-C. Yang DCY35.
67771<- DC Yang, Kyunghee Univ.

doi: 10.13145/bacdive11439.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Brevibacillus
  • species: Brevibacillus panacihumi
  • full scientific name: Brevibacillus panacihumi Kim et al. 2009

@ref: 16591

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Brevibacillus

species: Brevibacillus panacihumi

full scientific name: Brevibacillus panacihumi Kim et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28907positive7 µm0.45 µmrod-shapedyes
67771rod-shapedyes
67771positive
69480yes97.963
69480positive100

Culture and growth conditions

culture medium

  • @ref: 16591
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830; with strain-specific modifications) 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 MnSO4 Distilled water

culture temp

@refgrowthtypetemperaturerange
16591positivegrowth30mesophilic
28907positivegrowth15-42
28907positiveoptimum30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
28907positivegrowth05-09alkaliphile
28907positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
28907aerobe
67771aerobe

spore formation

@refspore formationtype of sporeconfidence
28907yes
67771yesendospore
69481yes93
69480yes100

halophily

  • @ref: 28907
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <2 %

observation

@refobservation
28907aggregates in clumps
67770quinones: MK-7
67771quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2890730089acetate+carbon source
2890717128adipate+carbon source
2890716449alanine+carbon source
2890724265gluconate+carbon source
2890725115malate+carbon source
2890729864mannitol+carbon source
2890737684mannose+carbon source
28907506227N-acetylglucosamine+carbon source
2890718401phenylacetate+carbon source
2890726271proline+carbon source
2890726546rhamnose+carbon source
2890731011valerate+carbon source
289074853esculin+hydrolysis

enzymes

@refvalueactivityec
28907acid phosphatase+3.1.3.2
28907alkaline phosphatase+3.1.3.1
28907arylsulfatase+3.1.6.1
28907catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
16591surface soil of a ginseng fieldRepublic of KoreaKORAsia
67770Soil of a ginseng fieldRepublic of KoreaKORAsia
67771From soilRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1006.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_95;96_577;97_674;98_783;99_1006&stattab=map
  • Last taxonomy: Brevibacillus
  • 16S sequence: EU383033
  • Sequence Identity:
  • Total samples: 646
  • soil counts: 304
  • aquatic counts: 105
  • animal counts: 138
  • plant counts: 99

Safety information

risk assessment

  • @ref: 16591
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16591
  • description: Brevibacillus panacihumi strain DCY35 16S ribosomal RNA gene, partial sequence
  • accession: EU383033
  • length: 1473
  • database: ena
  • NCBI tax ID: 497735

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brevibacillus panacihumi strain JCM 15085497735.10wgspatric497735
66792Brevibacillus panacihumi JCM 150852854289608draftimg497735
67770Brevibacillus panacihumi JCM 15085GCA_003710985contigncbi497735

GC content

@refGC-contentmethod
1659150.1
6777050.1high performance liquid chromatography (HPLC)
6777150.05

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes93no
gram-positiveyes83.632no
anaerobicno98.272yes
halophileno93.004no
spore-formingyes94.446yes
glucose-utilyes88.239no
aerobicyes81.523no
thermophileno93.634no
motileyes92.171yes
flagellatedyes62.734no
glucose-fermentno94.549no

External links

@ref: 16591

culture collection no.: DSM 22869, JCM 15085, KCTC 13206, DCY 35

straininfo link

  • @ref: 80677
  • straininfo: 404643

literature

  • topic: Phylogeny
  • Pubmed-ID: 19406823
  • title: Brevibacillus panacihumi sp. nov., a beta-glucosidase-producing bacterium.
  • authors: Kim MK, Sathiyaraj S, Pulla RK, Yang DC
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.001248-0
  • year: 2009
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/analysis/isolation & purification, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genotype, Gram-Positive Endospore-Forming Rods/*classification/genetics/isolation & purification/physiology, Korea, Molecular Sequence Data, *Panax, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, beta-Glucosidase/*biosynthesis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16591Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22869)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22869
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
28907Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2534628776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
80677Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404643.1StrainInfo: A central database for resolving microbial strain identifiers