Methanoculleus horonobensis (DSM 21626, JCM 15517, T10)

Name: Methanoculleus horonobensis (DSM 21626, JCM 15517, T10)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24159

Type strain

Strain Designation T10

Culture col. no. DSM 21626 JCM 15517 T10

NCBI tax ID(s) 528314

Special Collections DSMZ JCM Literature strains

History <- S. Shimizu, Horonobe Research Institute for the Subsurface Environment, Horonobe-cho, Hokkaido, Japan.; T10 S. Shimizu T10.

Links

Methanoculleus horonobensis T10 is an anaerobe, Gram-negative, ovoid-shaped archaeon that was isolated from deep aquifer water from a Miocene diatomaceous hard shale .

Gram-negative ovoid-shaped anaerobe genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 406551

JCM 15517,DSM 21626

@ref 20215

Last LPSN update 2026-02-09 11:23:54

Domain Archaea

Phylum Methanobacteriota

Class "Methanomicrobia"

Order Methanomicrobiales

Family Methanomicrobiaceae

Genus Methanoculleus

Species Methanoculleus horonobensis

Full scientific name Methanoculleus horonobensis Shimizu et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
31146	negative	1.15 µm	1.15 µm	ovoid-shaped
125439	negative					98.3

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21017	METHANOCULLEUS SP. MEDIUM (DSMZ Medium 141b)		Medium recipe at MediaDive	Name: METHANOCULLEUS SP. MEDIUM (DSMZ Medium 141b) Composition: NaHCO3 4.89237 g/l MgCl2 x 6 H2O 3.91389 g/l Yeast extract 1.95695 g/l Trypticase peptone 1.95695 g/l Na-acetate 0.978474 g/l Na2S x 9 H2O 0.489237 g/l L-Cysteine HCl x H2O 0.489237 g/l KCl 0.332681 g/l NH4Cl 0.244618 g/l K2HPO4 0.136986 g/l MgSO4 x 7 H2O 0.0293542 g/l Nitrilotriacetic acid 0.0146771 g/l NaCl 0.00978474 g/l MnSO4 x H2O 0.00489237 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00195695 g/l CoSO4 x 7 H2O 0.00176125 g/l ZnSO4 x 7 H2O 0.00176125 g/l FeSO4 x 7 H2O 0.000978474 g/l CaCl2 x 2 H2O 0.000978474 g/l Sodium resazurin 0.000489237 g/l NiCl2 x 6 H2O 0.000293542 g/l AlK(SO4)2 x 12 H2O 0.000195695 g/l CuSO4 x 5 H2O 9.78474e-05 g/l Pyridoxine hydrochloride 9.78474e-05 g/l Na2MoO4 x 2 H2O 9.78474e-05 g/l H3BO3 9.78474e-05 g/l Nicotinic acid 4.89237e-05 g/l Riboflavin 4.89237e-05 g/l (DL)-alpha-Lipoic acid 4.89237e-05 g/l Thiamine HCl 4.89237e-05 g/l Calcium D-(+)-pantothenate 4.89237e-05 g/l p-Aminobenzoic acid 4.89237e-05 g/l Folic acid 1.95695e-05 g/l Biotin 1.95695e-05 g/l Na2WO4 x 2 H2O 3.91389e-06 g/l Na2SeO3 x 5 H2O 2.93542e-06 g/l Vitamin B12 9.78474e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21017	positive	growth	37
31146	positive	growth	25-45
31146	positive	optimum	39.5
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH
31146	positive	optimum	6.75
31146	positive	growth	5.8-8.2

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
21017	anaerobe
31146	anaerobe
125438	anaerobe	90.433
125439	obligate anaerobe	99.2

Spore formation

@ref	Spore formation	Confidence
125439		96.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31146	NaCl	positive	growth	0-7.54 %
31146	NaCl	positive	optimum	0.87 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31146	15740 ChEBI	formate	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Groundwater
#Environmental	#Terrestrial	#Geologic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21017	deep aquifer water from a Miocene diatomaceous hard shale (Wakkanai formation)	Hokkaido, Horonobe	Japan	JPN	Asia
67770	Groundwater from a deep diatomaceous shale formation located in Horonobe	Hokkaido	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB436897 (>99% sequence identity) for Methanoculleus horonobensis subclade from Microbeatlas

Aquatic Samples	3
Soil Samples
Animal Samples	1
Plant Samples
Total Samples	4

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21017	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM160237v1 assembly for Methanoculleus horonobensis T10	contig	GCA_001602375	528314.3	2987171229	528314	75.48

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21017	Methanoculleus horonobensis gene for 16S rRNA, partial sequence	AB436897	1432		528314

GC content

@ref	GC-content (mol%)	Method
21017	62.9	high performance liquid chromatography (HPLC)
31146	62.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanoculleus horonobensis JCM 15517
NCBI: GCA_001602375

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.80	no
125439	motility	BacteriaNetⓘ	no	57.70	no
125439	gram_stain	BacteriaNetⓘ	negative	98.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methanoculleus horonobensis strain T10
PATRIC: 528314.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	71.62	yes
125438	anaerobic	anaerobicⓘ	yes	90.43	yes
125438	spore-forming	spore-formingⓘ	no	86.45	no
125438	aerobic	aerobicⓘ	no	89.09	yes
125438	thermophilic	thermophileⓘ	no	78.68	yes
125438	flagellated	motile2+ⓘ	no	85.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Identification and cultivation of anaerobic bacterial scavengers of dead cells.	Hirakata Y, Mei R, Morinaga K, Katayama T, Tamaki H, Meng XY, Watari T, Yamaguchi T, Hatamoto M, Nobu MK.	ISME J	10.1038/s41396-023-01538-2	2023
Enzymology	Structural Insights into the Methane-Generating Enzyme from a Methoxydotrophic Methanogen Reveal a Restrained Gallery of Post-Translational Modifications.	Kurth JM, Muller MC, Welte CU, Wagner T.	Microorganisms	10.3390/microorganisms9040837	2021
Genetics	Draft Genome Sequences of Methanoculleus horonobensis Strain JCM 15517, Methanoculleus thermophilus Strain DSM 2373, and Methanofollis ethanolicus Strain JCM 15103, Hydrogenotrophic Methanogens Belonging to the Family Methanomicrobiaceae.	Narihiro T, Kusada H, Yoneda Y, Tamaki H	Genome Announc	10.1128/genomeA.00199-16	2016
Phylogeny	Methanoculleus horonobensis sp. nov., a methanogenic archaeon isolated from a deep diatomaceous shale formation.	Shimizu S, Ueno A, Tamamura S, Naganuma T, Kaneko K	Int J Syst Evol Microbiol	10.1099/ijs.0.053520-0	2013

References

#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 )
#21017	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21626
#27474	IJSEM 4320 2013 ( DOI 10.1099/ijs.0.053520-0 , PubMed 23832970 )
#31146	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 #27474
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Methanoculleus horonobensis (DSM 21626, JCM 15517, T10)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001602375

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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