Thermogymnomonas acidicola (DSM 18835, JCM 13583, IC-189)

Name: Thermogymnomonas acidicola (DSM 18835, JCM 13583, IC-189)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 18138

Type strain

Strain Designation IC-189

Culture col. no. DSM 18835 JCM 13583 IC-189

NCBI tax ID(s) 1295120 399579

Special Collections DSMZ JCM

Links

Thermogymnomonas acidicola IC-189 is a thermophilic prokaryote that was isolated from solfataric soil.

thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 319398

DSM 18835,JCM 13583

@ref 20215

Last LPSN update 2025-12-16 09:51:16

Domain Methanobacteriati

Phylum Methanobacteriota

Class Thermoplasmata

Order Thermoplasmatales

Family [Thermoplasmatales, not assigned to family]

Genus Thermogymnomonas

Species Thermogymnomonas acidicola

Full scientific name Thermogymnomonas acidicola Itoh et al. 2007

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7731	THERMOGYMNOMONAS MEDIUM (DSMZ Medium 1141)		Medium recipe at MediaDive	Name: THERMOGYMNOMONAS MEDIUM (DSMZ Medium 1141) Composition: Glucose 10.0 g/l KH2PO4 3.0 g/l Yeast extract 1.0 g/l MgSO4 x 7 H2O 0.5 g/l CaCl2 x 2 H2O 0.25 g/l (NH4)2SO4 0.2 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7731	positive	growth	60	thermophilic
67770	positive	growth	60	thermophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	anaerobe	99.5

Observation

67770

Observationquinones: MK-7

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Environmental	#Terrestrial	#Volcanic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7731	solfataric soil	Kanagawa Prefecture,Hakone, Ohwaku-dani	Japan	JPN	Asia
67770	Solfataric soil collected from Ohwaku-dani	Hakone	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7731	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	ASM1464679v1 assembly for Thermogymnomonas acidicola JCM 13583	scaffold	GCA_014646795	399579.5		399579	72.89
67770	ASM131610v1 assembly for Thermogymnomonas acidicola JCM 13583	contig	GCA_001316105	1295120.7	2681813015	1295120	30.22

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7731	Thermogymnomonas acidicola gene for 16S rRNA, partial sequence	AB269873	1438		399579

GC content

@ref	GC-content (mol%)	Method
7731	56.1
67770	56.1	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: Thermogymnomonas acidicola JCM 13583
NCBI: GCA_014646795

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.50	no
125439	gram_stain	BacteriaNetⓘ	positive	64.10	no
125439	motility	BacteriaNetⓘ	yes	61.50	no
125439	spore_formation	BacteriaNetⓘ	yes	64.90	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Evolutionary patterns of archaea predominant in acidic environment.	Bargiela R, Korzhenkov AA, McIntosh OA, Toshchakov SV, Yakimov MM, Golyshin PN, Golyshina OV.	Environ Microbiome	10.1186/s40793-023-00518-5	2023
	Recurrent Potential G-Quadruplex Sequences in Archaeal Genomes.	Chashchina GV, Shchyolkina AK, Kolosov SV, Beniaminov AD, Kaluzhny DN.	Front Microbiol	10.3389/fmicb.2021.647851	2021
Pathogenicity	Effect of dietary fiber on the methanogen community in the hindgut of Lantang gilts.	Cao Z, Liang JB, Liao XD, Wright AD, Wu YB, Yu B.	Animal	10.1017/s1751731116000525	2016
	Phylogenetic distribution of DNA topoisomerase VI and its distinction from SPO11.	Allen AMB, Maxwell A.	NAR Genom Bioinform	10.1093/nargab/lqae085	2024
	Occurrence of Thermophilic Microorganisms in Different Full Scale Biogas Plants.	Kushkevych I, Cejnar J, Vitezova M, Vitez T, Dordevic D, Bomble YJ.	Int J Mol Sci	10.3390/ijms21010283	2019
	Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms.	Krause S, Bremges A, Munch PC, McHardy AC, Gescher J.	Sci Rep	10.1038/s41598-017-03315-6	2017
	Diversity of "Ca. Micrarchaeota" in Two Distinct Types of Acidic Environments and Their Associations with Thermoplasmatales.	Golyshina OV, Bargiela R, Toshchakov SV, Chernyh NA, Ramayah S, Korzhenkov AA, Kublanov IV, Golyshin PN.	Genes (Basel)	10.3390/genes10060461	2019
Phylogeny	Cuniculiplasmataceae, their ecogenomic and metabolic patterns, and interactions with 'ARMAN'.	Golyshina OV, Bargiela R, Golyshin PN.	Extremophiles	10.1007/s00792-018-1071-2	2019
Enzymology	Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles.	Wells M, Kim M, Akob DM, Basu P, Stolz JF.	Microbiol Spectr	10.1128/spectrum.04145-22	2023
Metabolism	Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota.	Chen LX, Mendez-Garcia C, Mendez-Garcia C, Dombrowski N, Servin-Garciduenas LE, Eloe-Fadrosh EA, Fang BZ, Luo ZH, Tan S, Zhi XY, Hua ZS, Martinez-Romero E, Woyke T, Huang LN, Sanchez J, Pelaez AI, Ferrer M, Baker BJ, Shu WS.	ISME J	10.1038/s41396-017-0002-z	2018
	A New Combination of Substrates: Biogas Production and Diversity of the Methanogenic Microorganisms.	Kushkevych I, Vitezova M, Vitez T, Kovac J, Kaucka P, Jesionek W, Bartos M, Barton L.	Open Life Sci	10.1515/biol-2018-0017	2018
Phylogeny	Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential.	Al-Amoudi S, Essack M, Simoes MF, Bougouffa S, Soloviev I, Archer JA, Lafi FF, Bajic VB.	Mar Drugs	10.3390/md14090165	2016
	Soil Microbiome Dynamics During Pyritic Mine Tailing Phytostabilization: Understanding Microbial Bioindicators of Soil Acidification.	Hottenstein JD, Neilson JW, Gil-Loaiza J, Root RA, White SA, Chorover J, Maier RM.	Front Microbiol	10.3389/fmicb.2019.01211	2019
Metabolism	Life in hot acid: pathway analyses in extremely thermoacidophilic archaea.	Auernik KS, Cooper CR, Kelly RM.	Curr Opin Biotechnol	10.1016/j.copbio.2008.08.001	2008
Metabolism	Molybdate treatment and sulfate starvation decrease ATP and DNA levels in Ferroplasma acidarmanu.	Baumler DJ, Hung KF, Jeong KC, Kaspar CW.	Archaea	10.1155/2008/762967	2008
Phylogeny	Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage.	Mendez-Garcia C, Mesa V, Sprenger RR, Richter M, Diez MS, Solano J, Bargiela R, Golyshina OV, Manteca A, Ramos JL, Gallego JR, Llorente I, Martins dos Santos VA, Jensen ON, Pelaez AI, Sanchez J, Ferrer M.	ISME J	10.1038/ismej.2013.242	2014
Genetics	Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea.	Yelton AP, Comolli LR, Justice NB, Castelle C, Denef VJ, Thomas BC, Banfield JF.	BMC Genomics	10.1186/1471-2164-14-485	2013
Metabolism	Characterization of variation in rumen methanogenic communities under different dietary and host feed efficiency conditions, as determined by PCR-denaturing gradient gel electrophoresis analysis.	Zhou M, Hernandez-Sanabria E, Guan LL.	Appl Environ Microbiol	10.1128/aem.00010-10	2010
Phylogeny	Oxyplasma meridianum gen. nov., sp. nov., an extremely acidophilic organotrophic member of the order Thermoplasmatales.	Golyshina OV, Lunev EA, Distaso MA, Bargiela R, Gaines MC, Daum B, Ferrer M, Bale NJ, Koenen M, Damste JSS, Yakimov MM, Golyshin PN.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006499	2024
Phylogeny	Thermogymnomonas acidicola gen. nov., sp. nov., a novel thermoacidophilic, cell wall-less archaeon in the order Thermoplasmatales, isolated from a solfataric soil in Hakone, Japan.	Itoh T, Yoshikawa N, Takashina T	Int J Syst Evol Microbiol	10.1099/ijs.0.65203-0	2007

References

#7731	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18835
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Thermogymnomonas acidicola (DSM 18835, JCM 13583, IC-189)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014646795

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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