Name: Methanosarcina horonobensis HB-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7131

Type strain:

Species: Methanosarcina horonobensis

Strain Designation: HB-1

Culture col. no.: DSM 21571, JCM 15518, NBRC 102577

Strain history: S. Shimizu HB-1.

NCBI tax ID(s): 1434110 (strain), 418008 (species)

SI-ID 401545

DSM 21571

Section

Methanosarcina horonobensis HB-1 is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from deep subsurface groundwater from a Miocene Wakkanai Formation aquifer consisting of siliceous mudstone.

Gram-negative
anaerobe
mesophilic
16S sequence
Archaea
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Archaea"
	Phylum	*Methanobacteriota*
	Class	"Methanomicrobia"
	Order	*Methanosarcinales*
	Family	*Methanosarcinaceae*
	Genus	*Methanosarcina*
	Species	**Methanosarcina horonobensis**
	Full Scientific Name (LPSN)	Methanosarcina horonobensis Shimizu et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.992

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15813]

Culture medium

METHANOSARCINA MEDIUM (DSMZ Medium 120)

[Ref.: #15813]

Culture medium growth

[Ref.: #15813]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15813]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #15813]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #15813]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #15813]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %98.65

[Ref.: #69481]	Ability of spore formation	no Confidence in %98
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.016

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

[Ref.: #15813]	Sample type/isolated from	deep subsurface groundwater from a Miocene Wakkanai Formation aquifer consisting of siliceous mudstone
[Ref.: #15813]	Geographic location (country and/or sea, region)	Horonobe, Hokkaido
[Ref.: #15813]	Country	Japan
[Ref.: #15813]	Country ISO 3 Code	JPN
[Ref.: #15813]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Groundwater sampled from a subsurface Miocene 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?

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

[Ref.: #15813]

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.: #15813]	Methanosarcina horonobensis gene for 16S rRNA, partial sequence	AB288262	1432	ENA	418008 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methanosarcina horonobensis HB-1 = JCM 15518	GCA_000970285	complete	GenBank	1434110 tax ID	*
[Ref.: #66792]	Methanosarcina horonobensis HB-1 = JCM 15518	GCA_001316205	contig	GenBank	1434110 tax ID	*
[Ref.: #66792]	Methanosarcina horonobensis JCM 15518	2684622506	draft	JGI IMG/M	1434110 tax ID	*
[Ref.: #66792]	Methanosarcina horonobensis HB-1	2627854269	complete	JGI IMG/M	1434110 tax ID	*
[Ref.: #66792]	Methanosarcina horonobensis HB-1 = JCM 15518	1434110.4	complete	PATRIC	1434110 tax ID	*
[Ref.: #66792]	Methanosarcina horonobensis HB-1 = JCM 15518	1434110.5	wgs	PATRIC	1434110 tax ID	*

[Ref.: #15813]	GC-content	41 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	41.4 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Methanosarcina horonobensis HB-1 = JCM 15518 HB-1 NCBI: GCA_000970285.1
[Ref.: #69481]	spore-forming	no	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Methanosarcina horonobensis HB-1 = JCM 15518 HB-1 NCBI: GCA_000970285.1
[Ref.: #69480]	motile	no	91.019	no
[Ref.: #69480]	flagellated	no	97.589	no
[Ref.: #69480]	gram-positive	no	96.187	no
[Ref.: #69480]	anaerobic	yes	97.818	yes
[Ref.: #69480]	aerobic	no	93.561	yes
[Ref.: #69480]	halophile	no	88.328	no
[Ref.: #69480]	spore-forming	no	95.1	no
[Ref.: #69480]	thermophile	no	98.541	no
[Ref.: #69480]	glucose-util	yes	67.933	no
[Ref.: #69480]	glucose-ferment	no	68.612	no

Availability in culture collections External links

[Ref.: #15813]

Culture collection no.

DSM 21571, JCM 15518, NBRC 102577

[Ref.: #76586]

SI-ID 401545

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Methanosarcina spelaei sp. nov., a methanogenic archaeon isolated from a floating biofilm of a subsurface sulphurous lake.	Ganzert L, Schirmack J, Alawi M, Mangelsdorf K, Sand W, Hillebrand-Voiculescu A, Wagner D	Int J Syst Evol Microbiol	10.1099/ijs.0.064956-0	2014	*
Phylogeny	Methanosarcina soligelidi sp. nov., a desiccation- and freeze-thaw-resistant methanogenic archaeon from a Siberian permafrost-affected soil.	Wagner D, Schirmack J, Ganzert L, Morozova D, Mangelsdorf K	Int J Syst Evol Microbiol	10.1099/ijs.0.046565-0	2013	*
Phylogeny	Methanosarcina horonobensis sp. nov., a methanogenic archaeon isolated from a deep subsurface Miocene formation.	Shimizu S, Upadhye R, Ishijima Y, Naganuma T	Int J Syst Evol Microbiol	10.1099/ijs.0.028548-0	2010	*

References

#15813

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21571

#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;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#76586

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-ID401545.1 )

* These data were automatically processed and therefore are not curated

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Methanosarcina horonobensis HB-1 = JCM 15518 HB-1

Methanosarcina horonobensis HB-1 = JCM 15518 HB-1

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