Name: Methanoculleus horonobensis T10
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24159

Type strain:

Species: Methanoculleus horonobensis

Strain Designation: T10

Culture col. no.: DSM 21626, JCM 15517

Strain history: S. Shimizu T10.

NCBI tax ID(s): 528314 (species)

SI-ID 406551

DSM 21626

Special Collections

Section

When using BacDive for research please cite our paper

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

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

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Archaea*
	Phylum	*Methanobacteriota*
	Class	"Methanomicrobia"
	Order	*Methanomicrobiales*
	Family	*Methanomicrobiaceae*
	Genus	*Methanoculleus*
	Species	**Methanoculleus horonobensis**
	Full Scientific Name (LPSN)	Methanoculleus horonobensis Shimizu et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #31146]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %98.3

[Ref.: #31146]	Cell length	1.15 µm

[Ref.: #31146]	Cell width	1.15 µm

[Ref.: #31146]	Cell shape	ovoid-shaped

[Ref.: #31146]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21017]

Culture medium

METHANOCULLEUS SP. MEDIUM (DSMZ Medium 141b)

[Ref.: #21017]

Culture medium growth

[Ref.: #21017]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21017]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21017]	growth	37 °C
[Ref.: #31146]	growth	25-45 °C
[Ref.: #31146]	optimum	39.5 °C
[Ref.: #67770]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #31146]			optimum	6.75
[Ref.: #31146]			growth	5.8-8.2

Information on physiology and metabolism Physiology and metabolism

[Ref.: #21017]	Oxygen tolerance	anaerobe
[Ref.: #31146]	Oxygen tolerance	anaerobe
[Ref.: #125438]	Oxygen tolerance	anaerobe Confidence in %90.433
[Ref.: #125439]	Oxygen tolerance	obligate anaerobe Confidence in %99.2

[Ref.: #125439]

Ability of spore formation

no Confidence in %96.8

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31146]		NaCl		growth	0-7.54	%
[Ref.: #31146]		NaCl		optimum	0.87	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31146]		formate ChEBI	+	carbon source

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

[Ref.: #21017]	Sample type/isolated from	deep aquifer water from a Miocene diatomaceous hard shale (Wakkanai formation)
[Ref.: #21017]	Geographic location (country and/or sea, region)	Hokkaido, Horonobe
[Ref.: #21017]	Country	Japan
[Ref.: #21017]	Country ISO 3 Code	JPN
[Ref.: #21017]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Groundwater from a deep diatomaceous shale formation located in Horonobe
[Ref.: #67770]	Geographic location (country and/or sea, region)	Hokkaido
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Groundwater
#Environmental	#Terrestrial	#Geologic

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #21017]

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.: #21017]	Methanoculleus horonobensis gene for 16S rRNA, partial sequence	AB436897	1432	GenBank ENA	528314 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Methanoculleus horonobensis JCM 15517	GCA_001602375	contig	GenBank ENA	528314 tax ID
[Ref.: #66792]	Methanoculleus horonobensis strain T10	528314.3	wgs	PATRIC	528314 tax ID	*

[Ref.: #21017]	GC-content	62.9 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31146]	GC-content	62.9 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methanoculleus horonobensis strain T10 PATRIC: 528314.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	71.621	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	90.433	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	86.445	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	89.085	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	78.675	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	85.5	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanoculleus horonobensis JCM 15517 NCBI: GCA_001602375
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	96.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	57.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	98.3
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate anaerobe	99.2

Availability in culture collections External links

[Ref.: #21017]

Culture collection no.

DSM 21626, JCM 15517

[Ref.: #88115]

SI-ID 406551

Literature:

Topic	Title	Authors	Journal	DOI	Year
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

#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 (see below)

#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;

#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 .

#88115

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-ID406551.1 )

#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 .

#27474

IJSEM 4320 2013 ( DOI 10.1099/ijs.0.053520-0 , PubMed 23832970 )

* These data were automatically processed and therefore are not curated

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Methanoculleus horonobensis strain T10

Methanoculleus horonobensis JCM 15517

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