Name: Methanosphaera stadtmanae MCB-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6980

Type strain:

Species: Methanosphaera stadtmanae

Strain Designation: MCB-3

Culture col. no.: DSM 3091, ATCC 43021, JCM 11832, OCM 149

Strain history: DSM 3091 <-- T. L. Miller MCB-3.

NCBI tax ID(s): 339860 (strain), 2317 (species)

SI-ID 47692

DSM 3091, ATCC 43021, JCM 11832

Section

Methanosphaera stadtmanae MCB-3 is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from human faeces.

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	*Methanobacteria*
	Order	*Methanobacteriales*
	Family	*Methanobacteriaceae*
	Genus	*Methanosphaera*
	Species	**Methanosphaera stadtmanae**
	Full Scientific Name (LPSN)	Methanosphaera stadtmanae corrig. Miller and Wolin 1985

Synonym

Methanosphaera stadtmaniae

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.951

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1297]

Culture medium

METHANOSPHAERA (MCB-3) MEDIUM (DSMZ Medium 322)

[Ref.: #1297]

Culture medium growth

[Ref.: #1297]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1297]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #1297]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #1297]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #1297]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.531

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.91

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	coenzyme M biosynthesis	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	methanofuran biosynthesis	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	valine 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]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	methanogenesis from CO2	66.67	8 of 12
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	vitamin B12 metabolism	64.71	22 of 34
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	photosynthesis	64.29	9 of 14
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	purine metabolism	60.64	57 of 94
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	pyrimidine metabolism	57.78	26 of 45
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	glutamate and glutamine metabolism	53.57	15 of 28
[Ref.: #66794]	peptidoglycan biosynthesis	53.33	8 of 15
[Ref.: #66794]	threonine metabolism	50	5 of 10
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	50	4 of 8
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	glycolysis	47.06	8 of 17
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	methionine metabolism	46.15	12 of 26
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	citric acid cycle	42.86	6 of 14
[Ref.: #66794]	tryptophan metabolism	42.11	16 of 38
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	oxidative phosphorylation	39.56	36 of 91
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	lysine metabolism	38.1	16 of 42
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	proline metabolism	36.36	4 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	35.71	5 of 14
[Ref.: #66794]	alanine metabolism	34.48	10 of 29
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	33.33	3 of 9
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	non-pathway related	31.58	12 of 38
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	isoprenoid biosynthesis	30.77	8 of 26
[Ref.: #66794]	propionate fermentation	30	3 of 10
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	ppGpp biosynthesis	25	1 of 4
[Ref.: #66794]	sulfopterin metabolism	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
		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.: #1297]	Sample type/isolated from	human faeces
[Ref.: #1297]	Country	USA
[Ref.: #1297]	Country ISO 3 Code	USA
[Ref.: #1297]	Continent	North America

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

Isolation sources categories

#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JQ346752 (>99% sequence identity) for Methanosphaera from Microbeatlas

Aquatic Samples	194
Soil Samples	76
Animal Samples	3685
Plant Samples	38
Total Samples	3993

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

[Ref.: #1297]

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.: #20218]	Methanosphaera stadtmanii 16S ribosomal RNA	M59139	1425	ENA	2317 tax ID	*
[Ref.: #20218]	Methanosphaera stadtmanae DSM 3091 strain MCB-3 16S ribosomal RNA gene, partial sequence	JQ346752	1267	ENA	339860 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methanosphaera stadtmanae DSM 3091	GCA_000012545	complete	GenBank	339860 tax ID	*
[Ref.: #66792]	Methanosphaera stadtmanae DSM 3091	637000163	complete	JGI IMG/M	339860 tax ID	*
[Ref.: #66792]	Methanosphaera stadtmanae DSM 3091	339860.19	complete	PATRIC	339860 tax ID	*

[Ref.: #1297]

GC-content

26.0 mol%

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: Methanosphaera stadtmanae DSM 3091 DSM 3091 NCBI: GCA_000012545.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Methanosphaera stadtmanae DSM 3091 DSM 3091 NCBI: GCA_000012545.1
[Ref.: #69480]	motile	no	93.405	no
[Ref.: #69480]	flagellated	no	97.253	no
[Ref.: #69480]	gram-positive	no	94.426	no
[Ref.: #69480]	anaerobic	yes	98.349	no
[Ref.: #69480]	halophile	no	88.487	no
[Ref.: #69480]	spore-forming	no	94.383	no
[Ref.: #69480]	thermophile	no	92.191	yes
[Ref.: #69480]	glucose-util	yes	66.513	no
[Ref.: #69480]	aerobic	no	95.231	yes
[Ref.: #69480]	glucose-ferment	no	54.366	no

Availability in culture collections External links

[Ref.: #1297]

Culture collection no.

DSM 3091, ATCC 43021, JCM 11832, OCM 149

[Ref.: #76441]

SI-ID 47692

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces.	Dridi B, Fardeau ML, Ollivier B, Raoult D, Drancourt M	Int J Syst Evol Microbiol	10.1099/ijs.0.033712-0	2012	*
Metabolism	High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol.	Dridi B, Henry M, El Khechine A, Raoult D, Drancourt M	PLoS One	10.1371/journal.pone.0007063	2009	*
Phylogeny	[Molecular diversity of rumen Archaea from Jinnan cattle].	Pei C, Mao S, Zhu W	Wei Sheng Wu Xue Bao		2008	*
Enzymology	Purification of the NADP+:F420 oxidoreductase of Methanosphaera stadtmanae.	Elias DA, Juck DF, Berry KA, Sparling R	Can J Microbiol		2000	*

References

#1297

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3091

#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 .

#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 )

#76441

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-ID47692.1 )

* These data were automatically processed and therefore are not curated

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Methanosphaera stadtmanae DSM 3091 DSM 3091

Methanosphaera stadtmanae DSM 3091 DSM 3091

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