Strain identifier

BacDive ID: 18022

Type strain: Yes

Species: Caldicellulosiruptor bescii

Strain Designation: Z-1320

Strain history: <- DSM <- VA Svetlichny, Z-1320

NCBI tax ID(s): 521460 (strain), 31899 (species)

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General

@ref: 2791

BacDive-ID: 18022

DSM-Number: 6725

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-positive, rod-shaped

description: Caldicellulosiruptor bescii Z-1320 is an anaerobe, thermophilic, Gram-positive bacterium that was isolated from hot spring.

NCBI tax id

NCBI tax idMatching level
31899species
521460strain

strain history

@refhistory
2791<- V.A. Svetlichny, Z-1320
67771<- DSM <- VA Svetlichny, Z-1320

doi: 10.13145/bacdive18022.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Syntrophomonadaceae
  • genus: Caldicellulosiruptor
  • species: Caldicellulosiruptor bescii
  • full scientific name: Caldicellulosiruptor bescii Yang et al. 2010

@ref: 2791

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridia, not assigned to family

genus: Caldicellulosiruptor

species: Caldicellulosiruptor bescii

full scientific name: Caldicellulosiruptor bescii Yang et al. 2010

strain designation: Z-1320

type strain: yes

Morphology

cell morphology

@refgram staincell shapeconfidence
43381positiverod-shaped
67771rod-shaped
67771positive
69480positive99.999

Culture and growth conditions

culture medium

  • @ref: 2791
  • name: ANAEROCELLUM MEDIUM (DSMZ Medium 516)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/516
  • composition: Name: ANAEROCELLUM MEDIUM (DSMZ Medium 516) Composition: Cellobiose 4.99002 g/l Na2CO3 1.49701 g/l Na2S x 9 H2O 0.499002 g/l Yeast extract 0.499002 g/l KCl 0.329341 g/l NH4Cl 0.329341 g/l KH2PO4 0.329341 g/l CaCl2 x 2 H2O 0.329341 g/l MgCl2 x 6 H2O 0.329341 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l CoCl2 x 6 H2O 0.000189621 g/l Pyridoxine hydrochloride 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l ZnCl2 6.98603e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l Biotin 1.99601e-05 g/l Folic acid 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
2791positivegrowth75thermophilic
43381positiveoptimum78-80hyperthermophilic
43381positivegrowth42-90hyperthermophilic
67771positivegrowth75thermophilic
69480thermophilic100

culture pH

  • @ref: 43381
  • ability: positive
  • type: growth
  • pH: 7.2

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
2791anaerobe
43381anaerobe
67771anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
43381no
69481no91
69480yes97.05

observation

@refobservation
43381growth on hardwood
43381growth on napier grass
43381growth on switchgrass

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4338130089acetate-growth
43381495055beta-cyclodextrin+assimilation
4338185146carboxymethylcellulose+assimilation
4338117057cellobiose+assimilation
4338162968cellulose+assimilation
4338162968cellulose+degradation
4338116261chitosan-growth
4338152071dextran-growth
4338117113erythritol-growth
4338128757fructose+assimilation
4338128260galactose+assimilation
4338117234glucose+assimilation
4338117754glycerol-growth
4338128087glycogen+assimilation
4338115443inulin-growth
4338130849L-arabinose+assimilation
4338124996lactate-growth
4338117716lactose+assimilation
4338117306maltose+assimilation
4338128808mannan-growth
4338129864mannitol+/-growth
4338137684mannose+assimilation
4338128053melibiose+assimilation
4338117309pectin+assimilation
4338162969polygalacturonic acid+/-growth
4338127941pullulan+assimilation
4338115361pyruvate-growth
4338116634raffinose+/-growth
4338126546rhamnose+assimilation
4338130911sorbitol+/-growth
4338128017starch+assimilation
4338117992sucrose+assimilation
4338127082trehalose+assimilation
4338137166xylan+assimilation
4338117151xylitol-growth
4338118222xylose+assimilation
43381yeast extract (0.01 %, w/v)+/-growth

metabolite production

@refChebi-IDmetaboliteproduction
4338130089acetateyes
4338116526carbon dioxideyes
4338118276dihydrogenyes
4338124996lactateyes

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
2791hot springKamchatka, Valley of GeysersRussiaRUSEurope
43381continental thermal springKamtchatkaRussiaRUSAsia1990
67771From hot springValley of Geysers, KamchatkaRussiaRUSAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Thermal spring
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2329.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_153;96_509;97_1491;98_1816;99_2329&stattab=map
  • Last taxonomy: Caldicellulosiruptor bescii subclade
  • 16S sequence: CP001393
  • Sequence Identity:
  • Total samples: 54
  • soil counts: 3
  • aquatic counts: 24
  • animal counts: 26
  • plant counts: 1

Safety information

risk assessment

  • @ref: 2791
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 67771
  • description: Caldicellulosiruptor bescii DSM 6725, complete genome
  • accession: CP001393
  • length: 2919718
  • database: ena
  • NCBI tax ID: 521460

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caldicellulosiruptor bescii DSM 6725GCA_000022325completencbi521460
66792Caldicellulosiruptor bescii DSM 6725521460.28plasmidpatric521460
66792Caldicellulosiruptor bescii DSM 6725521460.8completepatric521460
66792Caldicellulosiruptor bescii DSM 6725521460.29plasmidpatric521460
66792Caldicellulosiruptor bescii DSM 6725643692002completeimg521460

GC content

@refGC-content
279135.14
279136.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno91no
motileyes83.467no
flagellatedno85.247no
gram-positiveyes85.029yes
anaerobicyes99.465yes
aerobicno98.776yes
halophileno97.713no
spore-formingno76.132yes
glucose-utilyes88.528yes
thermophileyes100no
glucose-fermentyes51.255no

External links

@ref: 2791

culture collection no.: DSM 6725, ATCC BAA 1888, KCTC 15123, KCTC 4509, KCTC 4512

straininfo link

  • @ref: 87011
  • straininfo: 48280

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19801388Classification of 'Anaerocellum thermophilum' strain DSM 6725 as Caldicellulosiruptor bescii sp. nov.Yang SJ, Kataeva I, Wiegel J, Yin Y, Dam P, Xu Y, Westpheling J, Adams MWWInt J Syst Evol Microbiol10.1099/ijs.0.017731-02009Bacteria, Anaerobic/*classification/genetics/*isolation & purification/metabolism, Cellulose/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Hot Springs/microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Genetics21227922Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725.Dam P, Kataeva I, Yang SJ, Zhou F, Yin Y, Chou W, Poole FL 2nd, Westpheling J, Hettich R, Giannone R, Lewis DL, Kelly R, Gilbert HJ, Henrissat B, Xu Y, Adams MWNucleic Acids Res10.1093/nar/gkq12812011Bacterial Adhesion, Bacterial Proteins/genetics, Biomass, Carbohydrate Metabolism/*genetics, Gene Expression Profiling, Genes, Bacterial, *Genome, Bacterial, Genomics, Gram-Positive Bacteria/*genetics/metabolism/ultrastructure, Plants/metabolism, ProteomicsMetabolism
Enzymology21604181Identification and characterization of CbeI, a novel thermostable restriction enzyme from Caldicellulosiruptor bescii DSM 6725 and a member of a new subfamily of HaeIII-like enzymes.Chung DH, Huddleston JR, Farkas J, Westpheling JJ Ind Microbiol Biotechnol10.1007/s10295-011-0976-x2011Amino Acid Sequence, Deoxyribonucleases, Type II Site-Specific/classification/genetics/*metabolism, Enzyme Stability, Gram-Positive Bacteria/*enzymology/genetics, Molecular Sequence Data, Phylogeny, Sequence AlignmentPhylogeny
Metabolism22823185Enzymatic synthesis of piceid glucosides using maltosyltransferase from Caldicellulosiruptor bescii DSM 6725.Park H, Kim J, Choi KH, Hwang S, Yang SJ, Baek NI, Cha JJ Agric Food Chem10.1021/jf302127a2012Bacteria/*enzymology, Biological Availability, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, Escherichia coli/genetics/metabolism, Glucosides/*biosynthesis/chemistry, Glucosyltransferases/genetics/*metabolism, Magnetic Resonance Spectroscopy, Molecular Structure, Recombinant Proteins/genetics/metabolism, Resveratrol, Solubility, Stilbenes/chemistry/pharmacokinetics, alpha-Glucosidases/metabolismEnzymology
Metabolism22928042Methylation by a unique alpha-class N4-cytosine methyltransferase is required for DNA transformation of Caldicellulosiruptor bescii DSM6725.Chung D, Farkas J, Huddleston JR, Olivar E, Westpheling JPLoS One10.1371/journal.pone.00438442012Base Sequence, Biomass, *DNA Methylation, DNA, Bacterial/*genetics, DNA-Cytosine Methylases/*metabolism, Escherichia coli/genetics, Genetic Engineering/*methods, Genetic Loci/genetics, Thermoanaerobacterium/*enzymology/*genetics/metabolism, Transformation, Genetic/*geneticsGenetics
Enzymology24705464Cloning, expression and characterization of a novel thermophilic polygalacturonase from Caldicellulosiruptor bescii DSM 6725.Chen Y, Sun D, Zhou Y, Liu L, Han W, Zheng B, Wang Z, Zhang ZInt J Mol Sci10.3390/ijms150457172014Amino Acid Sequence, Bacterial Proteins/*genetics/metabolism, Cloning, Molecular, Escherichia coli/genetics, Gram-Positive Endospore-Forming Rods/*enzymology/*genetics/metabolism, Hot Temperature, Pectins/metabolism, Polygalacturonase/*genetics, Sequence AlignmentMetabolism
Enzymology31685873Biochemical characterisation of four rhamnosidases from thermophilic bacteria of the genera Thermotoga, Caldicellulosiruptor and Thermoclostridium.Baudrexl M, Schwarz WH, Zverlov VV, Liebl WSci Rep10.1038/s41598-019-52251-02019Bacterial Proteins/chemistry/*metabolism, Caldicellulosiruptor, Cloning, Molecular, Clostridiales/*enzymology, Cobalt/chemistry/metabolism, Edetic Acid/chemistry/metabolism, Firmicutes/*enzymology, Flavanones/metabolism, Glycoside Hydrolases/chemistry/*metabolism, Hydrogen-Ion Concentration, Inhibitory Concentration 50, Kinetics, Recombinant Proteins/biosynthesis/chemistry/isolation & purification, Rhamnose/metabolism, Substrate Specificity, Temperature, Thermotoga maritima/*enzymology, Thermotoga neapolitana/*enzymologyMetabolism
Phylogeny34542397Caldicellulosiruptor diazotrophicus sp. nov., a thermophilic, nitrogen-fixing fermentative bacterium isolated from a terrestrial hot spring in Japan.Chen Y, Nishihara A, Iino T, Ohkuma M, Haruta SInt J Syst Evol Microbiol10.1099/ijsem.0.0050142021Bacterial Typing Techniques, Base Composition, Caldicellulosiruptor, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Hot Springs, Japan, Nitrogen, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2791Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6725)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6725
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
43381Sung-Jae Yang, Irina Kataeva, Juergen Wiegel, Yanbin Yin, Phuogan Dam, Ying Xu, Janet Westpheling, Michael W. W. Adams10.1099/ijs.0.017731-0Classification of 'Anaerocellum thermophilum' strain DSM 6725 as Caldicellulosiruptor bescii sp. nov.IJSEM 60: 2011-2015 201019801388
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)
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
87011Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48280.1StrainInfo: A central database for resolving microbial strain identifiers