Methanospirillum lacunae (DSM 22751, JCM 16384, NBRC 104920)

Name: Methanospirillum lacunae (DSM 22751, JCM 16384, NBRC 104920)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7136

Type strain

Strain Designation Ki8-1

Culture col. no. DSM 22751 JCM 16384 NBRC 104920 Ki8-1

NCBI tax ID(s) 668570

Special Collections DSMZ JCM Literature strains

Links

Methanospirillum lacunae Ki8-1 is an anaerobe, mesophilic, Gram-negative prokaryote that was isolated from puddle soil.

Gram-negative motile rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402920

JCM 16384,NBRC 104920,DSM 22751

@ref 20215

Last LPSN update 2025-12-16 09:48:30

Domain Methanobacteriati

Phylum Methanobacteriota

Class "Methanomicrobia"

Order Methanomicrobiales

Family Methanospirillaceae

Genus Methanospirillum

Species Methanospirillum lacunae

Full scientific name Methanospirillum lacunae Iino et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
29752	negative	11-25 µm	0.5-0.6 µm	rod-shaped
125439	negative					98.5

Colony morphology

16493

Incubation period3-7 days

Pigmentation

29752

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16493	METHANOSPIRILLUM LACUNAE MEDIUM (DSMZ Medium 1273)		Medium recipe at MediaDive	Name: METHANOSPIRILLUM LACUNAE MEDIUM (DSMZ Medium 1273) Composition: Na2CO3 0.98912 g/l Na-acetate 0.791296 g/l NH4Cl 0.534125 g/l Na2S x 9 H2O 0.49456 g/l L-Cysteine HCl x H2O 0.49456 g/l MgCl2 x 6 H2O 0.197824 g/l Yeast extract 0.197824 g/l KH2PO4 0.138477 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l ZnSO4 x 7 H2O 0.00178042 g/l CoSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16493	positive	growth	30	mesophilic
29752	positive	growth	5-37
29752	positive	optimum	30	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
29752	positive	optimum	7.5
29752	positive	growth	6-9.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
16493	anaerobe
29752	anaerobe

Spore formation

@ref	Spore formation	Confidence
29752
125439		97.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29752	NaCl	positive	growth	0-1 %
29752	NaCl	positive	optimum	0-1 %

Observation

29752

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29752	15740 ChEBI	formate	+	carbon source

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	suberin monomers biosynthesis	100	2 of 2
66794	chorismate metabolism	100	9 of 9
66794	factor 420 biosynthesis	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	ribulose monophosphate pathway	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	glycine betaine biosynthesis	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	acetoin degradation	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	aspartate and asparagine metabolism	100	9 of 9
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	coenzyme M biosynthesis	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	methanofuran biosynthesis	80	4 of 5
66794	d-mannose degradation	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	palmitate biosynthesis	77.27	17 of 22
66794	phenylalanine metabolism	76.92	10 of 13
66794	purine metabolism	76.6	72 of 94
66794	pyrimidine metabolism	75.56	34 of 45
66794	methanogenesis from CO2	75	9 of 12
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	vitamin B12 metabolism	67.65	23 of 34
66794	nitrate assimilation	66.67	6 of 9
66794	serine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	oxidative phosphorylation	65.93	60 of 91
66794	methionine metabolism	65.38	17 of 26
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	heme metabolism	64.29	9 of 14
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	gluconeogenesis	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	threonine metabolism	60	6 of 10
66794	hydrogen production	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	glycine metabolism	60	6 of 10
66794	cellulose degradation	60	3 of 5
66794	starch degradation	60	6 of 10
66794	methylglyoxal degradation	60	3 of 5
66794	citric acid cycle	57.14	8 of 14
66794	lipid A biosynthesis	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	lysine metabolism	54.76	23 of 42
66794	arginine metabolism	54.17	13 of 24
66794	sulfate reduction	53.85	7 of 13
66794	alanine metabolism	51.72	15 of 29
66794	propionate fermentation	50	5 of 10
66794	cysteine metabolism	50	9 of 18
66794	non-pathway related	50	19 of 38
66794	sulfopterin metabolism	50	2 of 4
66794	tryptophan metabolism	50	19 of 38
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	kanosamine biosynthesis II	50	1 of 2
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	lipid metabolism	48.39	15 of 31
66794	propanol degradation	42.86	3 of 7
66794	lipoate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	urea cycle	38.46	5 of 13
66794	ketogluconate metabolism	37.5	3 of 8
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	proline metabolism	36.36	4 of 11
66794	vitamin B6 metabolism	36.36	4 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	pentose phosphate pathway	36.36	4 of 11
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	isoprenoid biosynthesis	30.77	8 of 26
66794	Entner Doudoroff pathway	30	3 of 10
66794	cardiolipin biosynthesis	28.57	2 of 7
66794	mevalonate metabolism	28.57	2 of 7
66794	peptidoglycan biosynthesis	26.67	4 of 15
66794	alginate biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	ppGpp biosynthesis	25	1 of 4
66794	degradation of pentoses	25	7 of 28
66794	androgen and estrogen metabolism	25	4 of 16
66794	vitamin E metabolism	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	carotenoid biosynthesis	22.73	5 of 22
66794	polyamine pathway	21.74	5 of 23

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	-
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16493	puddle soil	Chiba, Kisarazu	Japan	JPN	Asia
67770	Puddly soil in Kisarazu	Chiba	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB517986 (>99% sequence identity) for Methanospirillum lacunae subclade from Microbeatlas

Aquatic Samples	546
Soil Samples	95
Animal Samples	17
Plant Samples	23
Total Samples	681

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16493	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
67770	ASM317335v1 assembly for Methanospirillum lacunae Ki8-1	contig	GCA_003173355	668570.3	2994895097	668570	73.86

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16493	Methanospirillum lacunae gene for 16S ribosomal RNA, partial sequence	AB517986	1260		668570

GC content

@ref	GC-content (mol%)	Method
16493	45.3	high performance liquid chromatography (HPLC)
29752	45.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanospirillum lacunae Ki8-1
NCBI: GCA_003173355

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.90	no
125439	motility	BacteriaNetⓘ	no	77.00	no
125439	gram_stain	BacteriaNetⓘ	negative	98.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	66.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete genomes of the hydrogenotrophic methanogen species-Methanospirillum stamsii Pt1 and Methanospirillum lacunae Ki8-1.	Humm E, Chettiyar R, Rubbi L, Del Vecchio G, Pellegrini M, Ha SM, Gunsalus RP.	Microbiol Resour Announc	10.1128/mra.00736-25	2025
Phylogeny	Methanospirillum psychrodurum sp. nov., isolated from wetland soil.	Zhou L, Liu X, Dong X	Int J Syst Evol Microbiol	10.1099/ijs.0.057299-0	2013
Phylogeny	Methanospirillum stamsii sp. nov., a psychrotolerant, hydrogenotrophic, methanogenic archaeon isolated from an anaerobic expanded granular sludge bed bioreactor operated at low temperature.	Parshina SN, Ermakova AV, Bomberg M, Detkova EN	Int J Syst Evol Microbiol	10.1099/ijs.0.056218-0	2013
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

References

#16493	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22751
#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 )
#29752	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 #26134 (see below)
#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 .
#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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Methanospirillum lacunae (DSM 22751, JCM 16384, NBRC 104920)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003173355

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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