Caldanaerobacter subterraneus subsp. yonseiensis (DSM 13777, KFCC 11116, KB-1)

Name: Caldanaerobacter subterraneus subsp. yonseiensis (DSM 13777, KFCC 11116, KB-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16793

Type strain

Strain Designation KB-1

Culture col. no. DSM 13777 KFCC 11116 KB-1

NCBI tax ID(s) 111519

Special Collections DSMZ

History <- Y.-R. Pyun, Yonsei University, Seoul, Republic of Korea; KB-1 <- B.-C. Kim {1998}

Links

Caldanaerobacter subterraneus subsp. yonseiensis KB-1 is an anaerobe, thermophilic prokaryote that was isolated from mixed sample of mud and water from geothermal hot stream.

anaerobe thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 49522

DSM 13777

@ref 20215

Last LPSN update 2026-02-09 11:22:03

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Thermoanaerobacterales

Family Thermoanaerobacteraceae

Genus Caldanaerobacter

Species Caldanaerobacter subterraneus subsp. yonseiensis

Full scientific name Caldanaerobacter subterraneus subsp. yonseiensis (Kim et al. 2001) Fardeau et al. 2004

Synonyms (1)

Thermoanaerobacter yonseiensis

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5161	RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520)		Medium recipe at MediaDive	Name: RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520) Composition: Cellulose 9.97009 g/l (optional) Cellobiose 5.98205 g/l K2HPO4 x 3 H2O 2.89133 g/l Yeast extract 1.99402 g/l Na2CO3 1.49551 g/l KH2PO4 1.49551 g/l (NH4)2SO4 1.29611 g/l L-Cysteine HCl x H2O 0.498504 g/l MgCl2 x 6 H2O 0.199402 g/l CaCl2 x 2 H2O 0.0747757 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l FeSO4 x 7 H2O 0.00124626 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l H3BO3 5.98205e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5161	positive	growth	75	thermophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
5161	anaerobe
125438	anaerobe	95.814
125439	anaerobe	100

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Aquatic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5161	mixed sample of mud and water from geothermal hot stream	Java Island, Sileri	Indonesia	IDN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5161	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	TyKB-1 assembly for Caldanaerobacter subterraneus subsp. yonseiensis KB-1	contig	GCA_000473865	1388761.3	2563367176	1388761	55.14

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
5161	Caldanaerobacter subterraneus subsp. yonseiensis partial 16S rRNA gene, type strain DSM 13777T, clone 2	HG970170	1524	111519
5161	Caldanaerobacter subterraneus subsp. yonseiensis partial 16S rRNA gene, type strain DSM 13777T, clone 3	HG970171	1587	111519
5161	Caldanaerobacter subterraneus subsp. yonseiensis partial 16S rRNA gene, type strain DSM 13777T, clone 1	HG970169	1526	111519

GC content

@ref	GC-content (mol%)	Method
5161	37	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Caldanaerobacter subterraneus subsp. yonseiensis KB-1
NCBI: GCA_000473865

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	59.80	no
125439	motility	BacteriaNetⓘ	yes	72.20	no
125439	gram_stain	BacteriaNetⓘ	variable	81.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	100.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Caldanaerobacter subterraneus subsp. yonseiensis KB-1
PATRIC: 1388761.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	55.47	no
125438	anaerobic	anaerobicⓘ	yes	95.81	yes
125438	spore-forming	spore-formingⓘ	yes	71.08	no
125438	aerobic	aerobicⓘ	no	95.22	no
125438	thermophilic	thermophileⓘ	yes	81.24	yes
125438	flagellated	motile2+ⓘ	yes	74.30	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	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
Enzymology	A novel subtilisin-like serine protease from Thermoanaerobacter yonseiensis KB-1: its cloning, expression, and biochemical properties.	Jang HJ, Kim BC, Pyun YR, Kim YS	Extremophiles	10.1007/s00792-001-0248-1	2002
Phylogeny	Isolation from oil reservoirs of novel thermophilic anaerobes phylogenetically related to Thermoanaerobacter subterraneus: reassignment of T. subterraneus, Thermoanaerobacter yonseiensis, Thermoanaerobacter tengcongensis and Carboxydibrachium pacificum to Caldanaerobacter subterraneus gen. nov., sp. nov., comb. nov. as four novel subspecies.	Fardeau ML, Salinas MB, L'Haridon S, Jeanthon C, Verhe F, Cayol JL, Patel BKC, Garcia JL, Ollivier B	Int J Syst Evol Microbiol	10.1099/ijs.0.02711-0	2004
Phylogeny	Thermoanaerobacter yonseiensis sp. nov., a novel extremely thermophilic, xylose-utilizing bacterium that grows at up to 85 degrees C.	Kim BC, Grote R, Lee DW, Antranikian G, Pyun YR	Int J Syst Evol Microbiol	10.1099/00207713-51-4-1539	2001

References

#5161	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13777
#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 )
#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) .
#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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Caldanaerobacter subterraneus subsp. yonseiensis (DSM 13777, KFCC 11116, KB-1)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000473865

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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