Caldicellulosiruptor hydrothermalis (DSM 18901, VKM B-2411, 108)

Name: Caldicellulosiruptor hydrothermalis (DSM 18901, VKM B-2411, 108)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 18028

Type strain

Strain Designation 108

Culture col. no. DSM 18901 VKM B-2411 108 NBRC 117220

NCBI tax ID(s) 632292 413888

Special Collections DSMZ Literature strains

History DSMZ <- M. L. Miroshnichenko, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; 108 <- M. L. Miroshnichenko; {2003}

Links

Caldicellulosiruptor hydrothermalis 108 is an anaerobe, chemoorganoheterotroph, Gram-positive bacterium that was isolated from terrestrial neutral geothermal spring.

Gram-positive motile rod-shaped anaerobe chemoorganoheterotroph genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 397718

DSM 18901

@ref 20215

Last LPSN update 2026-05-29 08:29:09

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Caldicellulosiruptorales

Family Caldicellulosiruptoraceae

Genus Caldicellulosiruptor

Species Caldicellulosiruptor hydrothermalis

Full scientific name Caldicellulosiruptor hydrothermalis Miroshnichenko et al. 2008

Synonyms (1)

"Anaerocellum hydrothermalis"

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
32271	positive	3.1 µm	0.6 µm	rod-shaped
28511	positive	3-3.2 µm	0.5-0.7 µm	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7610	THERMOANAEROBACTER (BA) MEDIUM (DSMZ Medium 671)		Medium recipe at MediaDive	Name: THERMOANAEROBACTER (BA) MEDIUM (DSMZ Medium 671) Composition: Cellobiose 3.95648 g/l Cellulose 1.97824 g/l (optional) Na2CO3 0.98912 g/l NH4Cl 0.98912 g/l Yeast extract 0.74184 g/l K2HPO4 x 3 H2O 0.395648 g/l Na2S x 9 H2O 0.24728 g/l MgCl2 x 6 H2O 0.098912 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7610	positive	growth	65
28511	positive	optimum	65
28511	positive	growth	50-80
32271	positive	growth	50-80
32271	positive	optimum	65

Culture pH

@ref	Ability	Type	PH
32271	positive	optimum	7
28511	positive	optimum	7
32271	positive	growth	06-08
28511	positive	growth	6-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
7610	anaerobe
32271	anaerobe
28511	anaerobe
125438	anaerobe	97.728
125439	anaerobe	97.74

Nutrition type

28511

Typechemoorganoheterotroph

Spore formation

@ref	Spore formation
32271
28511

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32271	22599 ChEBI	arabinose	+	carbon source
28511	22599 ChEBI	arabinose	+	assimilation
28511	85146 ChEBI	carboxymethylcellulose	+	assimilation
32271	17057 ChEBI	cellobiose	+	carbon source
28511	17057 ChEBI	cellobiose	+	assimilation
28511	62968 ChEBI	cellulose	+	assimilation
28511	62968 ChEBI	cellulose	+	degradation
28511	17029 ChEBI	chitin	-	growth
28511	52071 ChEBI	dextran	+	assimilation
32271	28757 ChEBI	fructose	+	carbon source
28511	28757 ChEBI	fructose	+	assimilation
32271	28260 ChEBI	galactose	+	carbon source
28511	28260 ChEBI	galactose	+	assimilation
32271	17234 ChEBI	glucose	+	carbon source
28511	17234 ChEBI	glucose	+	assimilation
32271	17716 ChEBI	lactose	+	carbon source
28511	17716 ChEBI	lactose	+	assimilation
32271	17306 ChEBI	maltose	+	carbon source
28511	17306 ChEBI	maltose	+	assimilation
32271	29864 ChEBI	mannitol	+	carbon source
28511	29864 ChEBI	mannitol	+	assimilation
28511	17309 ChEBI	pectin	+	assimilation
28511		peptone	-	growth
28511	15361 ChEBI	pyruvate	-	growth
28511	16634 ChEBI	raffinose	-	growth
28511	33942 ChEBI	ribose	-	growth
28511	28017 ChEBI	starch	+	assimilation
32271	17992 ChEBI	sucrose	+	carbon source
28511	17992 ChEBI	sucrose	+	assimilation
28511	27082 ChEBI	trehalose	-	growth
28511	37166 ChEBI	xylan	+	assimilation
32271	18222 ChEBI	xylose	+	carbon source
28511	18222 ChEBI	xylose	+	assimilation
28511		yeast extract	+	assimilation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
28511	30089 ChEBI	acetate
28511	24996 ChEBI	lactate

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring
#Environmental	#Terrestrial	-
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7610	terrestrial neutral geothermal spring	Kamchatka	Russia	RUS	Asia
28511	neutral geothermal spring	Kamchatka	Russia	RUS	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF100908 (>99% sequence identity) for Caldicellulosiruptor hydrothermalis subclade from Microbeatlas

Aquatic Samples	10
Soil Samples	1
Animal Samples	0
Plant Samples	0
Total Samples	11

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7610	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM16635v1 assembly for Caldicellulosiruptor hydrothermalis 108	complete	GCA_000166355	632292.3	649633022	632292	99.61

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7610	Caldicellulosiruptor hydrothermalis strain 108 16S ribosomal RNA gene, partial sequence	EF100908	1482		632292

GC content

7610

GC-content (mol%)36.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM16635v1 assembly for Caldicellulosiruptor hydrothermalis 108
BV-BRC: 632292.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	97.74	no
125439	gram_stain	BacteriaNetⓘ	variable	66.70	no
125439	motility	BacteriaNetⓘ	yes	74.30	no
125439	spore_formation	BacteriaNetⓘ	yes	72.56	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Caldicellulosiruptor hydrothermalis 108 108
NCBI: GCA_000166355.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	75.52	yes
125438	anaerobic	anaerobicⓘ	yes	97.73	no
125438	aerobic	aerobicⓘ	no	98.01	yes
125438	spore-forming	spore-formingⓘ	no	64.63	yes
125438	thermophilic	thermophileⓘ	yes	82.72	yes
125438	flagellated	motile2+ⓘ	yes	72.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	A novel SfaNI-like restriction-modification system in Caldicellulosiruptor extents the genetic engineering toolbox for this genus.	Swinnen S, Zurek C, Kramer M, Heger RM, Domeyer JE, Ziegler J, Svetlitchnyi VA, Laufer A.	PLoS One	10.1371/journal.pone.0279562	2022
	Heterologous complementation of a pyrF deletion in Caldicellulosiruptor hydrothermalis generates a new host for the analysis of biomass deconstruction.	Groom J, Chung D, Young J, Westpheling J.	Biotechnol Biofuels	10.1186/s13068-014-0132-8	2014
	Fermentation of Mannitol Extracts From Brown Macro Algae by Thermophilic Clostridia.	Chades T, Scully SM, Ingvadottir EM, Orlygsson J.	Front Microbiol	10.3389/fmicb.2018.01931	2018
	Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement.	Chung D, Farkas J, Westpheling J.	Biotechnol Biofuels	10.1186/1754-6834-6-82	2013
	Multiplexed Assessment of Promiscuous Non-Canonical Amino Acid Synthase Activity in a Pyridoxal Phosphate-Dependent Protein Family.	Zmich A, Perkins LJ, Bingman C, Acheson JF, Buller AR.	ACS Catal	10.1021/acscatal.3c02498	2023
	Engineering Caldicellulosiruptor bescii with Surface Layer Homology Domain-Linked Glycoside Hydrolases Improves Plant Biomass Solubilization.	Laemthong T, Bing RG, Crosby JR, Adams MWW, Kelly RM.	Appl Environ Microbiol	10.1128/aem.01274-22	2022
	Biochemical and Structural Characterization of Thermostable GH159 Glycoside Hydrolases Exhibiting alpha-L-Arabinofuranosidase Activity.	Baudrexl M, Fida T, Berk B, Schwarz WH, Zverlov VV, Groll M, Liebl W.	Front Mol Biosci	10.3389/fmolb.2022.907439	2022
	Detection of a novel active transposable element in Caldicellulosiruptor hydrothermalis and a new search for elements in this genus.	Chung D, Farkas J, Westpheling J.	J Ind Microbiol Biotechnol	10.1007/s10295-013-1244-z	2013
Metabolism	Discovery of a Kojibiose Hydrolase by Analysis of Specificity-Determining Correlated Positions in Glycoside Hydrolase Family 65.	De Beul E, Jongbloet A, Franceus J, Desmet T.	Molecules	10.3390/molecules26206321	2021
Genetics	Complete genome sequences for the anaerobic, extremely thermophilic plant biomass-degrading bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor owensensis, and Caldicellulosiruptor lactoaceticus.	Blumer-Schuette SE, Ozdemir I, Mistry D, Lucas S, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Land ML, Hauser LJ, Woyke T, Mikhailova N, Pati A, Kyrpides NC, Ivanova N, Detter JC, Walston-Davenport K, Han S, Adams MW, Adams MW, Kelly RM.	J Bacteriol	10.1128/jb.01515-10	2011
Enzymology	The monofunctional CO dehydrogenase CooS is essential for growth of Thermoanaerobacter kivui on carbon monoxide.	Jain S, Katsyv A, Basen M, Muller V.	Extremophiles	10.1007/s00792-021-01251-y	2021
	Development of a pyrF-based counterselectable system for targeted gene deletion in Streptomyces rimosus.	Yang Y, Sun Q, Liu Y, Yin H, Yang W, Wang Y, Liu Y, Li Y, Pang S, Liu W, Zhang Q, Yuan F, Qiu S, Li J, Wang X, Fan K, Wang W, Li Z, Yin S.	J Zhejiang Univ Sci B	10.1631/jzus.b2000606	2021
	Parallel expansion and divergence of an adhesin family in pathogenic yeasts.	Smoak RA, Snyder LF, Fassler JS, He BZ.	Genetics	10.1093/genetics/iyad024	2023
Enzymology	Phylogenetic Diversity of Nitrogenase Reductase Genes and Possible Nitrogen-Fixing Bacteria in Thermophilic Chemosynthetic Microbial Communities in Nakabusa Hot Springs.	Nishihara A, Thiel V, Matsuura K, McGlynn SE, Haruta S.	Microbes Environ	10.1264/jsme2.me18030	2018
Metabolism	Deletion of a Peptidylprolyl Isomerase Gene Results in the Inability of Caldicellulosiruptor bescii To Grow on Crystalline Cellulose without Affecting Protein Glycosylation or Growth on Soluble Substrates.	Russell JF, Russo ML, Wang X, Hengge N, Chung D, Wells L, Bomble YJ, Westpheling J.	Appl Environ Microbiol	10.1128/aem.00909-20	2020
Transcriptome	Deletion of the Clostridium thermocellum recA gene reveals that it is required for thermophilic plasmid replication but not plasmid integration at homologous DNA sequences.	Groom J, Chung D, Kim SK, Guss A, Westpheling J.	J Ind Microbiol Biotechnol	10.1007/s10295-018-2049-x	2018
	Promiscuous plasmid replication in thermophiles: Use of a novel hyperthermophilic replicon for genetic manipulation of Clostridium thermocellum at its optimum growth temperature.	Groom J, Chung D, Olson DG, Lynd LR, Guss AM, Westpheling J.	Metab Eng Commun	10.1016/j.meteno.2016.01.004	2016
Metabolism	Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses.	Lee LL, Blumer-Schuette SE, Izquierdo JA, Zurawski JV, Loder AJ, Conway JM, Elkins JG, Podar M, Clum A, Jones PC, Piatek MJ, Weighill DA, Jacobson DA, Adams MWW, Kelly RM.	Appl Environ Microbiol	10.1128/aem.02694-17	2018
	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
Phylogeny	Caldicellulosiruptor kronotskyensis sp. nov. and Caldicellulosiruptor hydrothermalis sp. nov., two extremely thermophilic, cellulolytic, anaerobic bacteria from Kamchatka thermal springs.	Miroshnichenko ML, Kublanov IV, Kostrikina NA, Tourova TP, Kolganova TV, Birkeland NK, Bonch-Osmolovskaya EA	Int J Syst Evol Microbiol	10.1099/ijs.0.65236-0	2008

References

#7610	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18901
#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 )
#28511	IJSEM 1492 2008 ( DOI 10.1099/ijs.0.65236-0 , PubMed 18523201 )
#32271	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28511
#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) .
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Caldicellulosiruptor hydrothermalis (DSM 18901, VKM B-2411, 108)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Nutrition type

Spore formation

Metabolite utilization

Metabolite production

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000166355

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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