Name: Caldicellulosiruptor bescii Z-1320
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 18022

Type strain:

Species: Caldicellulosiruptor bescii

Strain Designation: Z-1320

Culture col. no.: DSM 6725, ATCC BAA-1888, KCTC 15123, KCTC 4509, KCTC 4512

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

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

SI-ID 48280

DSM 6725, ATCC BAA-1888

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Syntrophomonadaceae*
	Genus	*Caldicellulosiruptor*
	Species	**Caldicellulosiruptor bescii**
	Full Scientific Name (LPSN)	Caldicellulosiruptor bescii Yang et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #43381]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %99.999

[Ref.: #43381]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2791]

Culture medium

ANAEROCELLUM MEDIUM (DSMZ Medium 516)

[Ref.: #2791]

Culture medium growth

[Ref.: #2791]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2791]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #2791]	growth	75 °C
[Ref.: #43381]	optimum	78-80 °C
[Ref.: #43381]	growth	42-90 °C
[Ref.: #67771]	growth	75 °C

[Ref.: #2791]	Temperature range	thermophilic
[Ref.: #43381]	Temperature range	hyperthermophilic
[Ref.: #67771]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %100

	pH	Kind of pH		pH
[Ref.: #43381]			growth	7.2

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2791]	Oxygen tolerance	anaerobe
[Ref.: #43381]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %100

[Ref.: #43381]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %91
[Ref.: #69480]	Ability of spore formation	yes Confidence in %97.05

[Ref.: #43381]	Observation	growth on hardwood
[Ref.: #43381]	Observation	growth on napier grass
[Ref.: #43381]	Observation	growth on switchgrass

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43381]	acetate ChEBI	-	growth
[Ref.: #43381]	beta-cyclodextrin ChEBI	+	assimilation
[Ref.: #43381]	carboxymethylcellulose ChEBI	+	assimilation
[Ref.: #43381]	cellobiose ChEBI	+	assimilation
[Ref.: #43381]	cellulose ChEBI	+	assimilation
[Ref.: #43381]	cellulose ChEBI	+	degradation
[Ref.: #43381]	chitosan ChEBI	-	growth
[Ref.: #43381]	dextran ChEBI	-	growth
[Ref.: #43381]	erythritol ChEBI	-	growth
[Ref.: #43381]	fructose ChEBI	+	assimilation
[Ref.: #43381]	galactose ChEBI	+	assimilation
[Ref.: #43381]	glucose ChEBI	+	assimilation
[Ref.: #43381]	glycerol ChEBI	-	growth
[Ref.: #43381]	glycogen ChEBI	+	assimilation
[Ref.: #43381]	inulin ChEBI	-	growth
[Ref.: #43381]	L-arabinose ChEBI	+	assimilation
[Ref.: #43381]	lactate ChEBI	-	growth
[Ref.: #43381]	lactose ChEBI	+	assimilation
[Ref.: #43381]	maltose ChEBI	+	assimilation
[Ref.: #43381]	mannan ChEBI	-	growth
[Ref.: #43381]	mannitol ChEBI	+/-	growth
[Ref.: #43381]	mannose ChEBI	+	assimilation
[Ref.: #43381]	melibiose ChEBI	+	assimilation
[Ref.: #43381]	pectin ChEBI	+	assimilation
[Ref.: #43381]	polygalacturonic acid ChEBI	+/-	growth
[Ref.: #43381]	pullulan ChEBI	+	assimilation
[Ref.: #43381]	pyruvate ChEBI	-	growth
[Ref.: #43381]	raffinose ChEBI	+/-	growth
[Ref.: #43381]	rhamnose ChEBI	+	assimilation
[Ref.: #43381]	sorbitol ChEBI	+/-	growth
[Ref.: #43381]	starch ChEBI	+	assimilation
[Ref.: #43381]	sucrose ChEBI	+	assimilation
[Ref.: #43381]	trehalose ChEBI	+	assimilation
[Ref.: #43381]	xylan ChEBI	+	assimilation
[Ref.: #43381]	xylitol ChEBI	-	growth
[Ref.: #43381]	xylose ChEBI	+	assimilation
[Ref.: #43381]	yeast extract (0.01 %, w/v)	+/-	growth
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43381]	acetate ChEBI	yes
[Ref.: #43381]	carbon dioxide ChEBI	yes
[Ref.: #43381]	dihydrogen ChEBI	yes
[Ref.: #43381]	lactate ChEBI	yes

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #2791]	Sample type/isolated from	hot spring
[Ref.: #2791]	Geographic location (country and/or sea, region)	Kamchatka, Valley of Geysers
[Ref.: #2791]	Country	Russia
[Ref.: #2791]	Country ISO 3 Code	RUS
[Ref.: #2791]	Continent	Europe

[Ref.: #43381]	Sample type/isolated from	continental thermal spring
[Ref.: #43381]	Sampling date	1990
[Ref.: #43381]	Geographic location (country and/or sea, region)	Kamtchatka
[Ref.: #43381]	Country	Russia
[Ref.: #43381]	Country ISO 3 Code	RUS
[Ref.: #43381]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From hot spring
[Ref.: #67771]	Geographic location (country and/or sea, region)	Valley of Geysers, Kamchatka
[Ref.: #67771]	Country	Russia
[Ref.: #67771]	Country ISO 3 Code	RUS
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence CP001393 (>99% sequence identity) for Caldicellulosiruptor bescii subclade from Microbeatlas

Aquatic Samples	24
Soil Samples	3
Animal Samples	26
Plant Samples	1
Total Samples	54

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #2791]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67771]	Caldicellulosiruptor bescii DSM 6725, complete genome	CP001393	2919718	ENA	521460 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Caldicellulosiruptor bescii DSM 6725	GCA_000022325	complete	GenBank	521460 tax ID	*
[Ref.: #66792]	Caldicellulosiruptor bescii DSM 6725	521460.28	plasmid	PATRIC	521460 tax ID	*
[Ref.: #66792]	Caldicellulosiruptor bescii DSM 6725	521460.8	complete	PATRIC	521460 tax ID	*
[Ref.: #66792]	Caldicellulosiruptor bescii DSM 6725	521460.29	plasmid	PATRIC	521460 tax ID	*
[Ref.: #66792]	Caldicellulosiruptor bescii DSM 6725	643692002	complete	JGI IMG/M	521460 tax ID	*

[Ref.: #2791]	GC-content	35.14 mol%
[Ref.: #2791]	GC-content	36.7 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Caldicellulosiruptor bescii DSM 6725 DSM 6725 NCBI: GCA_000022325.1
[Ref.: #69481]	spore-forming	no	91	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Caldicellulosiruptor bescii DSM 6725 DSM 6725 NCBI: GCA_000022325.1
[Ref.: #69480]	motile	yes	83.467	no
[Ref.: #69480]	flagellated	no	85.247	no
[Ref.: #69480]	gram-positive	yes	85.029	yes
[Ref.: #69480]	anaerobic	yes	99.465	yes
[Ref.: #69480]	aerobic	no	98.776	yes
[Ref.: #69480]	halophile	no	97.713	no
[Ref.: #69480]	spore-forming	no	76.132	yes
[Ref.: #69480]	glucose-util	yes	88.528	yes
[Ref.: #69480]	thermophile	yes	100	no
[Ref.: #69480]	glucose-ferment	yes	51.255	no

Availability in culture collections External links

[Ref.: #2791]

Culture collection no.

DSM 6725, ATCC BAA-1888, KCTC 15123, KCTC 4509, KCTC 4512

[Ref.: #87011]

SI-ID 48280

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Biochemical characterisation of four rhamnosidases from thermophilic bacteria of the genera Thermotoga, Caldicellulosiruptor and Thermoclostridium.	Baudrexl M, Schwarz WH, Zverlov VV, Liebl W	Sci Rep	10.1038/s41598-019-52251-0	2019	*
Phylogeny	Caldicellulosiruptor 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 S	Int J Syst Evol Microbiol	10.1099/ijsem.0.005014	2021	*
Enzymology	Cloning, 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 Z	Int J Mol Sci	10.3390/ijms15045717	2014	*
Metabolism	Methylation 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 J	PLoS One	10.1371/journal.pone.0043844	2012	*
Metabolism	Enzymatic synthesis of piceid glucosides using maltosyltransferase from Caldicellulosiruptor bescii DSM 6725.	Park H, Kim J, Choi KH, Hwang S, Yang SJ, Baek NI, Cha J	J Agric Food Chem	10.1021/jf302127a	2012	*
Enzymology	Identification 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 J	J Ind Microbiol Biotechnol	10.1007/s10295-011-0976-x	2011	*
Genetics	Insights 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 MW	Nucleic Acids Res	10.1093/nar/gkq1281	2011	*
Phylogeny	Classification 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 MWW	Int J Syst Evol Microbiol	10.1099/ijs.0.017731-0	2009	*

References

#2791

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6725

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#43381

Sung-Jae Yang, Irina Kataeva, Juergen Wiegel, Yanbin Yin, Phuogan Dam, Ying Xu, Janet Westpheling, Michael W. W. Adams: Classification of 'Anaerocellum thermophilum' strain DSM 6725 as Caldicellulosiruptor bescii sp. nov.. IJSEM 60: 2011 - 2015 2010 ( DOI 10.1099/ijs.0.017731-0 , PubMed 19801388 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#69479

João 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 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#87011

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID48280.1 )

* These data were automatically processed and therefore are not curated

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Caldicellulosiruptor bescii DSM 6725 DSM 6725

Caldicellulosiruptor bescii DSM 6725 DSM 6725

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