Name: Methanospirillum hungatei JF-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7132

Type strain:

Species: Methanospirillum hungatei

Strain Designation: JF-1, JF1

Culture col. no.: DSM 864, ATCC 27890, JCM 10133, OCM 16, NBRC 100397

Strain history: DSM 864 <-- M. P. Bryant <-- J. G. Ferry JF1.

NCBI tax ID(s): 323259 (strain), 2203 (species)

SI-ID 47281

DSM 864, ATCC 27890, JCM 10133, NBRC 100397

Special Collections

DSMZ
JCM

Other strains from Methanospirillum hungatei

Section

When using BacDive for research please cite our paper

Methanospirillum hungatei JF-1 is an anaerobe, mesophilic archaeon that was isolated from sewage sludge.

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	*Methanospirillaceae*
	Genus	*Methanospirillum*
	Species	**Methanospirillum hungatei**
	Full Scientific Name (LPSN)	Methanospirillum hungatei corrig. Ferry et al. 1974 (Approved Lists 1980)

Synonym

Methanospirillum hungatii

Information on culture and growth conditions Culture and growth conditions

[Ref.: #467]

Culture medium

MODIFIED METHANOBACTERIUM MEDIUM (DSMZ Medium 1523)

[Ref.: #467]

Culture medium growth

[Ref.: #467]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #467]

Culture medium

METHANOBACTERIUM MEDIUM (DSMZ Medium 119)

[Ref.: #467]

Culture medium growth

[Ref.: #467]

Culture medium link

Medium recipe at MediaDive

[Ref.: #467]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #467]			growth	37 °C
[Ref.: #67770]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #467]	Oxygen tolerance	anaerobe
[Ref.: #125438]	Oxygen tolerance	anaerobe Confidence in %90.852
[Ref.: #125439]	Oxygen tolerance	anaerobe Confidence in %94.6

[Ref.: #125439]

Ability of spore formation

no Confidence in %92.9

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	factor 420 biosynthesis	100	5 of 5
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	methanofuran biosynthesis	80	4 of 5
[Ref.: #66794]	coenzyme M biosynthesis	80	8 of 10
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	methanogenesis from CO2	75	9 of 12
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	purine metabolism	73.4	69 of 94
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	lipid A biosynthesis	55.56	5 of 9
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	oxidative phosphorylation	53.85	49 of 91
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	alanine metabolism	51.72	15 of 29
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	tryptophan metabolism	44.74	17 of 38
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	isoprenoid biosynthesis	34.62	9 of 26
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	cardiolipin biosynthesis	28.57	2 of 7
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	26.67	4 of 15
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	ppGpp biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	glutathione metabolism	21.43	3 of 14
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #467]	Sample type/isolated from	sewage sludge
[Ref.: #467]	Country	USA
[Ref.: #467]	Country ISO 3 Code	USA
[Ref.: #467]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Sewage sludge
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Sewage sludge

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence M60880 (>99% sequence identity) for Methanospirillum hungatei subclade from Microbeatlas

Aquatic Samples	628
Soil Samples	36
Animal Samples	20
Plant Samples	86
Total Samples	770

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

[Ref.: #467]

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.: #67770]	Methanospirillum hungatei gene for 16S ribosomal RNA, partial sequence	AB517987	1259	GenBank ENA	323259 tax ID
[Ref.: #20218]	M.hungatei 16S ribosomal RNA	M60880	1466	GenBank ENA	2203 tax ID	*
[Ref.: #20218]	Methanospirillum hungatei JF-1 culture DSM:864 16S ribosomal RNA gene, partial sequence	JQ346747	1271	GenBank ENA	323259 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methanospirillum hungatei JF-1	GCA_000013445	complete	GenBank ENA	323259 tax ID	*
[Ref.: #66792]	Methanospirillum hungatei JF-1	637000164	complete	JGI IMG/M	323259 tax ID	*
[Ref.: #66792]	Methanospirillum hungatei JF-1	323259.15	complete	PATRIC	323259 tax ID	*

[Ref.: #467]	GC-content	45.0 mol%
[Ref.: #67770]	GC-content	45 mol%	Buoyant density centrifugation (BD)

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: Methanospirillum hungatei JF-1 JF-1 NCBI: GCA_000013445.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	70.059	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	90.852	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	91.57	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	85.943	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	83.646	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	85.208	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanospirillum hungatei JF-1 IMG: 637000164
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	92.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	79.3
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	64.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	94.6

Availability in culture collections External links

[Ref.: #467]

Culture collection no.

DSM 864, ATCC 27890, JCM 10133, OCM 16, NBRC 100397

[Ref.: #76587]

SI-ID 47281

Literature:

Only first 10 entries are displayed. Click here to see all.

	Title	Authors	Journal	DOI	Year
Genetics	Complete genome sequence of Methanospirillum hungatei type strain JF1.	Gunsalus RP, Cook LE, Crable B, Rohlin L, McDonald E, Mouttaki H, Sieber JR, Poweleit N, Zhou H, Lapidus AL, Daligault HE, Land M, Gilna P, Ivanova N, Kyrpides N, Culley DE, McInerney MJ	Stand Genomic Sci	10.1186/s40793-015-0124-8	2016	*
Phylogeny	Isolation and characterization of Flexilinea flocculi gen. nov., sp. nov., a filamentous, anaerobic bacterium belonging to the class Anaerolineae in the phylum Chloroflexi.	Sun L, Toyonaga M, Ohashi A, Matsuura N, Tourlousse DM, Meng XY, Tamaki H, Hanada S, Cruz R, Yamaguchi T, Sekiguchi Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.000822	2015	*
Phylogeny	Lactivibrio alcoholicus gen. nov., sp. nov., an anaerobic, mesophilic, lactate-, alcohol-, carbohydrate- and amino-acid-degrading bacterium in the phylum Synergistetes.	Qiu YL, Hanada S, Kamagata Y, Guo RB, Sekiguchi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.060681-0	2014	*
Metabolism	Mercury methylation by the methanogen Methanospirillum hungatei.	Yu RQ, Reinfelder JR, Hines ME, Barkay T	Appl Environ Microbiol	10.1128/AEM.01556-13	2013	*
Metabolism	Metabolism of H2 by Desulfovibrio alaskensis G20 during syntrophic growth on lactate.	Li X, McInerney MJ, Stahl DA, Krumholz LR	Microbiology (Reading)	10.1099/mic.0.051284-0	2011	*
Phylogeny	Methanospirillum lacunae sp. nov., a methane-producing archaeon isolated from a puddly soil, and emended descriptions of the genus Methanospirillum and Methanospirillum hungatei.	Iino T, Mori K, Suzuki KI	Int J Syst Evol Microbiol	10.1099/ijs.0.020131-0	2009	*
Phylogeny	Genomic characterization of methanomicrobiales reveals three classes of methanogens.	Anderson I, Ulrich LE, Lupa B, Susanti D, Porat I, Hooper SD, Lykidis A, Sieprawska-Lupa M, Dharmarajan L, Goltsman E, Lapidus A, Saunders E, Han C, Land M, Lucas S, Mukhopadhyay B, Whitman WB, Woese C, Bristow J, Kyrpides N	PLoS One	10.1371/journal.pone.0005797	2009	*
Phylogeny	The first true obligately syntrophic propionate-oxidizing bacterium, Pelotomaculum schinkii sp. nov., co-cultured with Methanospirillum hungatei, and emended description of the genus Pelotomaculum.	de Bok FAM, Harmsen HJM, Plugge CM, de Vries MC, Akkermans ADL, de Vos WM, Stams AJM	Int J Syst Evol Microbiol	10.1099/ijs.0.02880-0	2005	*
Phylogeny	Victivallis vadensis gen. nov., sp. nov., a sugar-fermenting anaerobe from human faeces.	Zoetendal EG, Plugge CM, Akkermans ADL, de Vos WM	Int J Syst Evol Microbiol	10.1099/ijs.0.02362-0	2003	*
Phylogeny	Desulfovirga adipica gen. nov., sp. nov., an adipate-degrading, gram-negative, sulfate-reducing bacterium.	Tanaka K, Stackebrandt E, Tohyama S, Eguchi T	Int J Syst Evol Microbiol	10.1099/00207713-50-2-639	2000	*
Phylogeny	Phylogenetic analyses of some extremely halophilic archaea isolated from Dead Sea water, determined on the basis of their 16S rRNA sequences.	Arahal DR, Dewhirst FE, Paster BJ, Volcani BE, Ventosa A	Appl Environ Microbiol	10.1128/aem.62.10.3779-3786.1996	1996	*
	The Sheaths of Methanospirillum Are Made of a New Type of Amyloid Protein.	Christensen LFB, Hansen LM, Finster K, Christiansen G, Nielsen PH, Otzen DE, Dueholm MS	Front Microbiol	10.3389/fmicb.2018.02729	2018	*
	Regulation of Product Formation in Bacteroides xylanolyticus X5-1 by Interspecies Electron Transfer.	Biesterveld S, Zehnder AJ, Stams AJ	Appl Environ Microbiol	10.1128/aem.60.4.1347-1352.1994	1994	*

References

#467	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 864

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 .

#76587

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-ID47281.1 )

#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 .

* These data were automatically processed and therefore are not curated

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