Strain identifier

BacDive ID: 3812

Type strain: Yes

Species: Leadbetterella byssophila

Strain Designation: 4M15

Strain history: KACC 11308 <-- H.-Y. Weon 4M15.

NCBI tax ID(s): 649349 (strain), 316068 (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: 6779

BacDive-ID: 3812

DSM-Number: 17132

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Leadbetterella byssophila 4M15 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from cotton waste compost.

NCBI tax id

NCBI tax idMatching level
316068species
649349strain

strain history

@refhistory
6779<- S.-W. Kwon <- H.-Y. Weon; 4M15
67770KACC 11308 <-- H.-Y. Weon 4M15.

doi: 10.13145/bacdive3812.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Leadbetterella
  • species: Leadbetterella byssophila
  • full scientific name: Leadbetterella byssophila Weon et al. 2005

@ref: 6779

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Leadbetterella

species: Leadbetterella byssophila

full scientific name: Leadbetterella byssophila Weon et al. 2005 emend. Hahnke et al. 2016

strain designation: 4M15

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31525negative4.5 µm0.75 µmrod-shapedno
69480no96.004
69480negative99.996

colony morphology

  • @ref: 27819
  • colony color: orange
  • medium used: TSA

pigmentation

@refproductionname
31525yes
27819yesFlexirubin

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_17132_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6779TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
27819Trypticase Soy Agar (TSA)yes

culture temp

@refgrowthtypetemperaturerange
6779positivegrowth30mesophilic
31525positivegrowth15-45
31525positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
31525positivegrowth06-08
31525positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31525
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.986

halophily

@refsaltgrowthtested relationconcentration
31525NaClpositivegrowth0-1 %
31525NaClpositiveoptimum0.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3152521217L-alaninamide+carbon source
3152516449alanine+carbon source
3152540585alpha-cyclodextrin+carbon source
31525286442-oxopentanoate+carbon source
3152522599arabinose+carbon source
3152518403L-arabitol+carbon source
3152535391aspartate+carbon source
3152517057cellobiose+carbon source
3152523652dextrin+carbon source
3152528757fructose+carbon source
3152533984fucose+carbon source
3152528260galactose+carbon source
3152524175galacturonate+carbon source
3152517234glucose+carbon source
3152529987glutamate+carbon source
3152528087glycogen+carbon source
3152517716lactose+carbon source
3152517306maltose+carbon source
3152537684mannose+carbon source
3152528053melibiose+carbon source
3152537657methyl D-glucoside+carbon source
3152551850methyl pyruvate+carbon source
31525506227N-acetylglucosamine+carbon source
3152518257ornithine+carbon source
3152516634raffinose+carbon source
3152526546rhamnose+carbon source
3152517814salicin+carbon source
3152517822serine+carbon source
3152517992sucrose+carbon source
3152526986threonine+carbon source
3152517748thymidine+carbon source
3152527082trehalose+carbon source
3152553424tween 20+carbon source
3152516704uridine+carbon source
315254853esculin+hydrolysis
278192509agar-hydrolysis
2781985146carboxymethylcellulose-hydrolysis
27819casein-degradation
27819casein-hydrolysis
2781962968cellulose-degradation
2781917029chitin-degradation
2781916991dna-degradation
278194853esculin+degradation
278195291gelatin+degradation
278195291gelatin+hydrolysis
2781917632nitrate-reduction
2781928017starch+degradation
2781928017starch+hydrolysis
2781953424tween 20+degradation
2781953423tween 40-degradation
2781953426tween 80-degradation
2781918186tyrosine+degradation

metabolite production

  • @ref: 31525
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 31525
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
31525acid phosphatase+3.1.3.2
31525alkaline phosphatase+3.1.3.1
31525alpha-galactosidase+3.2.1.22
31525catalase+1.11.1.6
31525cytochrome oxidase+1.9.3.1
27819arginine dihydrolase-3.5.3.6
27819leucine arylamidase+3.4.11.1
27819valine arylamidase+
27819naphthol-AS-BI-phosphohydrolase+
27819alpha-glucosidase+3.2.1.20
27819beta-glucosidase+3.2.1.21
27819N-acetyl-beta-glucosaminidase+3.2.1.52
27819alpha-fucosidase+3.2.1.51
27819alpha-galactosidase+/-3.2.1.22
27819beta-galactosidase+/-3.2.1.23

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6779cotton waste compostRepublic of KoreaKORAsia
67770Cotton-waste composts used as oyster mushroom cultivationRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Engineered#Biodegradation#Composting
#Engineered#Waste#Solid plant waste
#Host#Plants#Shrub (Scrub)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6916.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_608;96_3249;97_3987;98_5088;99_6916&stattab=map
  • Last taxonomy: Leadbetterella byssophila subclade
  • 16S sequence: AY854022
  • Sequence Identity:
  • Total samples: 5146
  • soil counts: 947
  • aquatic counts: 1993
  • animal counts: 2059
  • plant counts: 147

Safety information

risk assessment

  • @ref: 6779
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6779
  • description: Leadbetterella byssophila strain 4M15 16S ribosomal RNA gene, partial sequence
  • accession: AY854022
  • length: 1457
  • database: ena
  • NCBI tax ID: 649349

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leadbetterella byssophila DSM 17132GCA_000166395completencbi649349
66792Leadbetterella byssophila DSM 17132649349.3completepatric649349
66792Leadbetterella byssophila 4M15, DSM 17132649633063completeimg649349

GC content

@refGC-contentmethod
677933.0
3152533
677940.4sequence analysis
6777033high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.644yes
flagellatedno97.663yes
gram-positiveno97.941no
anaerobicno98.799yes
aerobicyes87.619yes
halophileno94.958yes
spore-formingno95.045no
thermophileno98.586yes
glucose-utilyes86.584yes
glucose-fermentno86.11no

External links

@ref: 6779

culture collection no.: DSM 17132, KACC 11308, JCM 16389, NBRC 106382

straininfo link

  • @ref: 73323
  • straininfo: 281446

literature

  • topic: Phylogeny
  • Pubmed-ID: 16280486
  • title: Leadbetterella byssophila gen. nov., sp. nov., isolated from cotton-waste composts for the cultivation of oyster mushroom.
  • authors: Weon HY, Kim BY, Kwon SW, Park IC, Cha IB, Tindall BJ, Stackebrandt E, Truper HG, Go SJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63741-0
  • year: 2005
  • mesh: Animals, Cytophagaceae/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Gossypium/microbiology, Industrial Waste/analysis, Molecular Sequence Data, Phylogeny, Pleurotus/*physiology, RNA, Ribosomal, 16S/analysis/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlepubmedID_cross_referencejournal
6779Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17132)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17132
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
2781910.1099/ijs.0.63741-016280486
31525Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127819
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
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
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.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
73323Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID281446.1StrainInfo: A central database for resolving microbial strain identifiers