Methanosphaera stadtmanae (DSM 3091, ATCC 43021, JCM 11832)

Name: Methanosphaera stadtmanae (DSM 3091, ATCC 43021, JCM 11832)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6980

Type strain

Strain Designation MCB-3

Culture col. no. DSM 3091 ATCC 43021 JCM 11832 MCB-3 OCM 149

NCBI tax ID(s) 339860 2317

Special Collections DSMZ JCM

History <- T. L. Miller, New York State Department of Health, Albany, New York, USA; MCB-3 (Methanosphaera stadtmaniae) DSM 3091 <-- T. L. Miller MCB-3.

Links

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

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 47692

DSM 3091,ATCC 43021,JCM 11832

@ref 20215

Last LPSN update 2025-12-16 09:48:27

Domain Methanobacteriati

Phylum Methanobacteriota

Class Methanobacteria

Order Methanobacteriales

Family Methanobacteriaceae

Genus Methanosphaera

Species Methanosphaera stadtmanae

Full scientific name Methanosphaera stadtmanae corrig. Miller and Wolin 1985

Synonyms (1)

Methanosphaera stadtmaniae

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	90.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1297	METHANOSPHAERA MEDIUM (DSMZ Medium 322)		Medium recipe at MediaDive	Name: METHANOSPHAERA MEDIUM (DSMZ Medium 322) Composition: Methanol 7.70428 g/l NaHCO3 3.89105 g/l KH2PO4 2.72374 g/l Trypticase peptone 1.94553 g/l Yeast extract 1.94553 g/l NH4Cl 0.972763 g/l NaCl 0.583658 g/l K2HPO4 0.583658 g/l Na-acetate 0.486381 g/l Na-formate 0.486381 g/l DL-Dithiothreitol 0.486381 g/l (NH4)2SO4 0.291829 g/l MgSO4 x 7 H2O 0.145914 g/l CaCl2 x 2 H2O 0.077821 g/l Nitrilotriacetic acid 0.0145914 g/l MnSO4 x H2O 0.00486381 g/l FeSO4 x 7 H2O 0.00291829 g/l Na2SeO4 0.00184825 g/l ZnSO4 x 7 H2O 0.00175097 g/l CoSO4 x 7 H2O 0.00175097 g/l NiCl2 x 6 H2O 0.000680934 g/l Sodium resazurin 0.000486381 g/l AlK(SO4)2 x 12 H2O 0.000194553 g/l Pyridoxine hydrochloride 0.000194553 g/l CuSO4 x 5 H2O 9.72763e-05 g/l (DL)-alpha-Lipoic acid 9.72763e-05 g/l H3BO3 9.72763e-05 g/l Thiamine HCl 9.72763e-05 g/l Riboflavin 9.72763e-05 g/l Nicotinic acid 9.72763e-05 g/l Calcium D-(+)-pantothenate 9.72763e-05 g/l p-Aminobenzoic acid 9.72763e-05 g/l Na2MoO4 x 2 H2O 9.72763e-05 g/l Biotin 3.89105e-05 g/l Folic acid 3.89105e-05 g/l Na2WO4 x 2 H2O 3.89105e-06 g/l Na2SeO3 x 5 H2O 2.91829e-06 g/l Vitamin B12 1.94553e-06 g/l Distilled water H2SO4

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
1297	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
1297	anaerobe
125438	anaerobe	90.277
125439	facultative anaerobe	91.4

Spore formation

@ref	Spore formation	Confidence
125439		97.9

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	ribulose monophosphate pathway	100	2 of 2
66794	coenzyme M biosynthesis	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	hydrogen production	80	4 of 5
66794	methanofuran biosynthesis	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	palmitate biosynthesis	77.27	17 of 22
66794	phenylalanine metabolism	76.92	10 of 13
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	vitamin B1 metabolism	69.23	9 of 13
66794	octane oxidation	66.67	2 of 3
66794	methanogenesis from CO2	66.67	8 of 12
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	d-mannose degradation	66.67	6 of 9
66794	NAD metabolism	66.67	12 of 18
66794	vitamin B12 metabolism	64.71	22 of 34
66794	heme metabolism	64.29	9 of 14
66794	photosynthesis	64.29	9 of 14
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	purine metabolism	60.64	57 of 94
66794	lipid metabolism	58.06	18 of 31
66794	pyrimidine metabolism	57.78	26 of 45
66794	propanol degradation	57.14	4 of 7
66794	serine metabolism	55.56	5 of 9
66794	nitrate assimilation	55.56	5 of 9
66794	arginine metabolism	54.17	13 of 24
66794	glutamate and glutamine metabolism	53.57	15 of 28
66794	peptidoglycan biosynthesis	53.33	8 of 15
66794	threonine metabolism	50	5 of 10
66794	glycogen biosynthesis	50	2 of 4
66794	adipate degradation	50	1 of 2
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	acetate fermentation	50	2 of 4
66794	C4 and CAM-carbon fixation	50	4 of 8
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	histidine metabolism	48.28	14 of 29
66794	glycolysis	47.06	8 of 17
66794	leucine metabolism	46.15	6 of 13
66794	methionine metabolism	46.15	12 of 26
66794	cysteine metabolism	44.44	8 of 18
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	mevalonate metabolism	42.86	3 of 7
66794	citric acid cycle	42.86	6 of 14
66794	tryptophan metabolism	42.11	16 of 38
66794	myo-inositol biosynthesis	40	4 of 10
66794	oxidative phosphorylation	39.56	36 of 91
66794	degradation of hexoses	38.89	7 of 18
66794	urea cycle	38.46	5 of 13
66794	lysine metabolism	38.1	16 of 42
66794	ketogluconate metabolism	37.5	3 of 8
66794	pentose phosphate pathway	36.36	4 of 11
66794	vitamin B6 metabolism	36.36	4 of 11
66794	proline metabolism	36.36	4 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	tetrahydrofolate metabolism	35.71	5 of 14
66794	alanine metabolism	34.48	10 of 29
66794	cyanate degradation	33.33	1 of 3
66794	CO2 fixation in Crenarchaeota	33.33	3 of 9
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	non-pathway related	31.58	12 of 38
66794	sulfate reduction	30.77	4 of 13
66794	isoprenoid biosynthesis	30.77	8 of 26
66794	propionate fermentation	30	3 of 10
66794	Entner Doudoroff pathway	30	3 of 10
66794	degradation of pentoses	28.57	8 of 28
66794	glutathione metabolism	28.57	4 of 14
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	polyamine pathway	26.09	6 of 23
66794	butanoate fermentation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	ppGpp biosynthesis	25	1 of 4
66794	sulfopterin metabolism	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	ascorbate metabolism	22.73	5 of 22

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
1297	human faeces	USA	USA	North America
67770	Human feces

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1297	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
66792	ASM1254v1 assembly for Methanosphaera stadtmanae DSM 3091	complete	GCA_000012545	339860.19	637000163	339860	99.46

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Methanosphaera stadtmanae DSM 3091 culture DSM:3091 16S ribosomal RNA gene, partial sequence	JQ346752	1267		339860
20218	Methanosphaera stadtmanii 16S ribosomal RNA	M59139	1425		2317

GC content

1297

GC-content (mol%)26.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanosphaera stadtmanae DSM 3091
IMG: 637000163

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.90	no
125439	motility	BacteriaNetⓘ	yes	54.10	no
125439	gram_stain	BacteriaNetⓘ	negative	90.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	91.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methanosphaera stadtmanae DSM 3091 DSM 3091
NCBI: GCA_000012545.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	64.67	no
125438	anaerobic	anaerobicⓘ	yes	90.28	no
125438	aerobic	aerobicⓘ	no	89.00	yes
125438	spore-forming	spore-formingⓘ	no	89.90	no
125438	thermophilic	thermophileⓘ	no	82.88	yes
125438	flagellated	motile2+ⓘ	no	84.96	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Microbiome-informed study of the mechanistic basis of methane inhibition by Asparagopsis taxiformis in dairy cattle.	Indugu N, Narayan K, Stefenoni HA, Hennessy ML, Vecchiarelli B, Bender JS, Shah R, Dai G, Garapati S, Yarish C, Welchez SC, Raisanen SE, Wasson D, Lage C, Melgar A, Hristov AN, Pitta DW.	mBio	10.1128/mbio.00782-24	2024
	Effects of fecal microbiota transplantation on the abundance and diversity of selected fungal and archaeal species in the gut microbiota in the rat model of schizophrenia.	Krawczyk A, Kasperski T, Gosiewski T, Nikiforuk A, Potasiewicz A, Arent Z, Salamon D.	Pharmacol Rep	10.1007/s43440-025-00793-8	2025
Metabolism	Rumen microbial degradation of bromoform from red seaweed (Asparagopsis taxiformis) and the impact on rumen fermentation and methanogenic archaea.	Romero P, Belanche A, Jimenez E, Hueso R, Ramos-Morales E, Salwen JK, Kebreab E, Yanez-Ruiz DR.	J Anim Sci Biotechnol	10.1186/s40104-023-00935-z	2023
Metabolism	The hydrogen threshold of obligately methyl-reducing methanogens.	Feldewert C, Lang K, Brune A.	FEMS Microbiol Lett	10.1093/femsle/fnaa137	2020
Phylogeny	Diversity and community of methanogens in the large intestine of finishing pigs.	Mi J, Peng H, Wu Y, Wang Y, Liao X.	BMC Microbiol	10.1186/s12866-019-1459-x	2019
	Meconial Methanobrevibacter smithii suggests intrauterine methanogen colonization in preterm neonates.	Sereme Y, Guindo CO, Filleron A, Corbeau P, Tran TA, Drancourt M, Vitte J, Grine G.	Curr Res Microb Sci	10.1016/j.crmicr.2021.100034	2021
	Proteomic and metabolomic profiling of extracellular vesicles produced by human gut archaea	Weinberger V, Darnhofer B, Thapa H, Mertelj P, Stentz R, Jones E, Grabmann G, Mohammadzadeh R, Shinde T, Karner C, Ober J, Juodeikis R, Pernitsch D, Hingerl K, Zurabishvili T, Kumpitsch C, Kuehnast T, Rinner B, Strohmaier H, Kolb D, Gotts K, Weichhart T, Kocher T, Kofeler H, Carding S, Schild S, Moissl-Eichinger C.	Nat Commun		2025
	Methanogenic Archaea in the Pediatric Inflammatory Bowel Disease in Relation to Disease Type and Activity.	Cisek AA, Szymanska E, Wierzbicka-Rucinska A, Aleksandrzak-Piekarczyk T, Cukrowska B.	Int J Mol Sci	10.3390/ijms25010673	2024
Enzymology	The Characterization of Ancient Methanococcales Malate Dehydrogenases Reveals That Strong Thermal Stability Prevents Unfolding Under Intense gamma-Irradiation.	Madern D, Halgand F, Houee-Levin C, Dufour AB, Coquille S, Ansanay-Alex S, Sacquin-Mora S, Brochier-Armanet C.	Mol Biol Evol	10.1093/molbev/msae231	2024
Genetics	Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics.	Basile A, Heinken A, Hertel J, Smarr L, Li W, Treu L, Valle G, Campanaro S, Thiele I.	Gut Microbes	10.1080/19490976.2023.2226921	2023
	The sanitary indoor environment-a potential source for intact human-associated anaerobes.	Pausan MR, Blohs M, Mahnert A, Moissl-Eichinger C.	NPJ Biofilms Microbiomes	10.1038/s41522-022-00305-z	2022
	Oral amoxicillin treatment disrupts the gut microbiome and metabolome without interfering with luminal redox potential in the intestine of Wistar Han rats.	Bermudez-Sanchez S, Bahl MI, Hansen EB, Licht TR, Laursen MF.	FEMS Microbiol Ecol	10.1093/femsec/fiaf003	2025
	Methanogens and Hydrogen Sulfide Producing Bacteria Guide Distinct Gut Microbe Profiles and Irritable Bowel Syndrome Subtypes.	Villanueva-Millan MJ, Leite G, Wang J, Morales W, Parodi G, Pimentel ML, Barlow GM, Mathur R, Rezaie A, Sanchez M, Ayyad S, Cohrs D, Chang C, Rashid M, Hosseini A, Fiorentino A, Weitsman S, Chuang B, Chang B, Pichetshote N, Pimentel M.	Am J Gastroenterol	10.14309/ajg.0000000000001997	2022
	The Human-Associated Archaeon Methanosphaera stadtmanae Is Recognized through Its RNA and Induces TLR8-Dependent NLRP3 Inflammasome Activation.	Vierbuchen T, Bang C, Rosigkeit H, Schmitz RA, Heine H.	Front Immunol	10.3389/fimmu.2017.01535	2017
	Evolving understanding of rumen methanogen ecophysiology.	Khairunisa BH, Heryakusuma C, Ike K, Mukhopadhyay B, Susanti D.	Front Microbiol	10.3389/fmicb.2023.1296008	2023
	Biofilm formation of mucosa-associated methanoarchaeal strains.	Bang C, Ehlers C, Orell A, Prasse D, Spinner M, Gorb SN, Albers SV, Schmitz RA.	Front Microbiol	10.3389/fmicb.2014.00353	2014
Pathogenicity	Microbiome Markers in Gastrointestinal Disorders: Inflammatory Bowel Disease, Colorectal Cancer, and Celiac Disease.	San-Martin MI, Chamizo-Ampudia A, Sanchiz A, Ferrero MA, Martinez-Blanco H, Rodriguez-Aparicio LB, Navasa N.	Int J Mol Sci	10.3390/ijms26104818	2025
	Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis).	Gruninger RJ, McAllister TA, Forster RJ.	PLoS One	10.1371/journal.pone.0156457	2016
	Alterations in intestinal Archaea composition in pediatric patients with Crohn's disease based on next-generation sequencing - a pilot study.	Krawczyk A, Gosiewski T, Zapala B, Kowalska-Duplaga K, Salamon D.	Gut Microbes	10.1080/19490976.2023.2276806	2023
Metabolism	CD Obesity-Prone Rats, but not Obesity-Resistant Rats, Robustly Ferment Resistant Starch Without Increased Weight or Fat Accretion.	Obanda D, Page R, Guice J, Raggio AM, Husseneder C, Marx B, Stout RW, Welsh DA, Taylor CM, Luo M, Blanchard EE, Bendiks Z, Coulon D, Keenan MJ.	Obesity (Silver Spring)	10.1002/oby.22120	2018
	The intestinal archaea Methanosphaera stadtmanae and Methanobrevibacter smithii activate human dendritic cells.	Bang C, Weidenbach K, Gutsmann T, Heine H, Schmitz RA.	PLoS One	10.1371/journal.pone.0099411	2014
Pathogenicity	Tungsten-enhanced growth of Methanosphaera stadtmanae.	Dridi B, Khelaifia S, Fardeau ML, Ollivier B, Drancourt M.	BMC Res Notes	10.1186/1756-0500-5-238	2012
Genetics	Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome.	Duller S, Vrbancic S, Szydlowski L, Mahnert A, Blohs M, Predl M, Kumpitsch C, Zrim V, Hogenauer C, Kosciolek T, Schmitz RA, Eberhard A, Dragovan M, Schmidberger L, Zurabischvili T, Weinberger V, Moser AM, Kolb D, Pernitsch D, Mohammadzadeh R, Kuhnast T, Rattei T, Moissl-Eichinger C.	Nat Commun	10.1038/s41467-024-52037-7	2024
Enzymology	A Reduced F₄₂₀-Dependent Nitrite Reductase in an Anaerobic Methanotrophic Archaeon.	Heryakusuma C, Susanti D, Yu H, Li Z, Purwantini E, Hettich RL, Orphan VJ, Mukhopadhyay B.	J Bacteriol	10.1128/jb.00078-22	2022
Genetics	Acute appendicitis manifests as two microbiome state types with oral pathogens influencing severity.	Blohs M, Mahnert A, Brunnader K, Flucher C, Castellani C, Till H, Singer G, Moissl-Eichinger C.	Gut Microbes	10.1080/19490976.2022.2145845	2023
Genetics	GenomeFingerprinter: the genome fingerprint and the universal genome fingerprint analysis for systematic comparative genomics.	Ai Y, Ai H, Meng F, Zhao L.	PLoS One	10.1371/journal.pone.0077912	2013
Phylogeny	Comparative Genomic Analysis of Members of the Genera Methanosphaera and Methanobrevibacter Reveals Distinct Clades with Specific Potential Metabolic Functions.	Poehlein A, Schneider D, Soh M, Daniel R, Seedorf H.	Archaea	10.1155/2018/7609847	2018
	Inhibition of Rumen Methanogens by a Novel Archaeal Lytic Enzyme Displayed on Tailored Bionanoparticles.	Altermann E, Schofield LR, Ronimus RS, Beatty AK, Reilly K.	Front Microbiol	10.3389/fmicb.2018.02378	2018
Pathogenicity	In-vitro archaeacidal activity of biocides against human-associated archaea.	Khelaifia S, Brunel JM, Drancourt M.	PLoS One	10.1371/journal.pone.0062738	2013
	Bile acid metabolism and signaling: Emerging pharmacological targets of dietary polyphenols.	Tveter KM, Mezhibovsky E, Wu Y, Roopchand DE.	Pharmacol Ther	10.1016/j.pharmthera.2023.108457	2023
Metabolism	Community composition and density of methanogens in the foregut of the Tammar wallaby (Macropus eugenii).	Evans PN, Hinds LA, Sly LI, McSweeney CS, Morrison M, Wright AD.	Appl Environ Microbiol	10.1128/aem.02436-08	2009
Phylogeny	A 'universal' type II chaperonin PCR detection system for the investigation of Archaea in complex microbial communities.	Chaban B, Hill JE.	ISME J	10.1038/ismej.2011.96	2012
Metabolism	Archaea and the human gut: new beginning of an old story.	Gaci N, Borrel G, Tottey W, O'Toole PW, Brugere JF.	World J Gastroenterol	10.3748/wjg.v20.i43.16062	2014
	Enteric methane emission of dairy cows supplemented with iodoform in a dose-response study.	Thorsteinsson M, Lund P, Weisbjerg MR, Noel SJ, Schonherz AA, Hellwing ALF, Hansen HH, Nielsen MO.	Sci Rep	10.1038/s41598-023-38149-y	2023
	The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the Methanomassiliicoccales.	Li Y, Leahy SC, Jeyanathan J, Henderson G, Cox F, Altermann E, Kelly WJ, Lambie SC, Janssen PH, Rakonjac J, Attwood GT.	Stand Genomic Sci	10.1186/s40793-016-0183-5	2016
Metabolism	Ribosomal intergenic spacer analysis as a tool for monitoring methanogenic Archaea changes in an anaerobic digester.	Ciesielski S, Bulkowska K, Dabrowska D, Kaczmarczyk D, Kowal P, Mozejko J.	Curr Microbiol	10.1007/s00284-013-0353-2	2013
Metabolism	Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease.	Heinken A, Ravcheev DA, Baldini F, Heirendt L, Fleming RMT, Thiele I.	Microbiome	10.1186/s40168-019-0689-3	2019
Metabolism	A vaccine against rumen methanogens can alter the composition of archaeal populations.	Williams YJ, Popovski S, Rea SM, Skillman LC, Toovey AF, Northwood KS, Wright AD.	Appl Environ Microbiol	10.1128/aem.02453-08	2009
Phenotype	Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires.	Bauer E, Laczny CC, Magnusdottir S, Wilmes P, Thiele I.	Microbiome	10.1186/s40168-015-0121-6	2015
Metabolism	Biochemical Characterisation of Phage Pseudomurein Endoisopeptidases PeiW and PeiP Using Synthetic Peptides.	Schofield LR, Beattie AK, Tootill CM, Dey D, Ronimus RS.	Archaea	10.1155/2015/828693	2015
Enzymology	Identification and characterization of gshA, a gene encoding the glutamate-cysteine ligase in the halophilic archaeon Haloferax volcanii.	Malki L, Yanku M, Borovok I, Cohen G, Mevarech M, Aharonowitz Y.	J Bacteriol	10.1128/jb.00297-09	2009
Genetics	DOOR: a database for prokaryotic operons.	Mao F, Dam P, Chou J, Olman V, Xu Y.	Nucleic Acids Res	10.1093/nar/gkn757	2009
	Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis.	Zuo G, Xu Z, Hao B.	Life (Basel)	10.3390/life5010949	2015
Metabolism	An intertwined evolutionary history of methanogenic archaea and sulfate reduction.	Susanti D, Mukhopadhyay B.	PLoS One	10.1371/journal.pone.0045313	2012
Genetics	Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves.	Fujishima K, Sugahara J, Tomita M, Kanai A.	PLoS One	10.1371/journal.pone.0001622	2008
Metabolism	Metabolism of Oxo-Bile Acids and Characterization of Recombinant 12alpha-Hydroxysteroid Dehydrogenases from Bile Acid 7alpha-Dehydroxylating Human Gut Bacteria.	Doden H, Sallam LA, Devendran S, Ly L, Doden G, Daniel SL, Alves JMP, Ridlon JM.	Appl Environ Microbiol	10.1128/aem.00235-18	2018
Pathogenicity	Effects of antimicrobial peptides on methanogenic archaea.	Bang C, Schilhabel A, Weidenbach K, Kopp A, Goldmann T, Gutsmann T, Schmitz RA.	Antimicrob Agents Chemother	10.1128/aac.00661-12	2012
	Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine.	Borrel G, Parisot N, Harris HM, Peyretaillade E, Gaci N, Tottey W, Bardot O, Raymann K, Gribaldo S, Peyret P, O'Toole PW, Brugere JF.	BMC Genomics	10.1186/1471-2164-15-679	2014
Phylogeny	Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families.	Petitjean C, Makarova KS, Wolf YI, Koonin EV.	Genome Biol Evol	10.1093/gbe/evx189	2017
Genetics	Gene capture coupled to high-throughput sequencing as a strategy for targeted metagenome exploration.	Denonfoux J, Parisot N, Dugat-Bony E, Biderre-Petit C, Boucher D, Morgavi DP, Le Paslier D, Peyretaillade E, Peyret P.	DNA Res	10.1093/dnares/dst001	2013
	Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes.	Dos Santos PC, Fang Z, Mason SW, Setubal JC, Dixon R.	BMC Genomics	10.1186/1471-2164-13-162	2012
Metabolism	Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales.	Sakai S, Takaki Y, Shimamura S, Sekine M, Tajima T, Kosugi H, Ichikawa N, Tasumi E, Hiraki AT, Shimizu A, Kato Y, Nishiko R, Mori K, Fujita N, Imachi H, Takai K.	PLoS One	10.1371/journal.pone.0022898	2011
Phylogeny	An antimethanogenic nutritional intervention in early life of ruminants modifies ruminal colonization by Archaea.	Abecia L, Waddams KE, Martinez-Fernandez G, Martin-Garcia AI, Ramos-Morales E, Newbold CJ, Yanez-Ruiz DR.	Archaea	10.1155/2014/841463	2014
Metabolism	An uncharacterized member of the ribokinase family in Thermococcus kodakarensis exhibits myo-inositol kinase activity.	Sato T, Fujihashi M, Miyamoto Y, Kuwata K, Kusaka E, Fujita H, Miki K, Atomi H.	J Biol Chem	10.1074/jbc.m113.457259	2013
Genetics	Role of Shwachman-Bodian-Diamond syndrome protein in translation machinery and cell chemotaxis: a comparative genomics approach.	Vasieva O.	Adv Appl Bioinform Chem	10.2147/aabc.s23510	2011
Genetics	Tracing lifestyle adaptation in prokaryotic genomes.	Altermann E.	Front Microbiol	10.3389/fmicb.2012.00048	2012
Genetics	Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin.	Perez-Rueda E, Janga SC.	Mol Biol Evol	10.1093/molbev/msq033	2010
	TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus.	Gorlas A, Koonin EV, Bienvenu N, Prieur D, Geslin C.	Environ Microbiol	10.1111/j.1462-2920.2011.02662.x	2012
	Oxygen and hydrogen peroxide in the early evolution of life on earth: in silico comparative analysis of biochemical pathways.	Slesak I, Slesak H, Kruk J.	Astrobiology	10.1089/ast.2011.0704	2012
Metabolism	Beating the acetyl coenzyme A-pathway to the origin of life.	Nitschke W, Russell MJ.	Philos Trans R Soc Lond B Biol Sci	10.1098/rstb.2012.0258	2013
	Solution (sup13)C Nuclear Magnetic Resonance Spectroscopic Analysis of the Amino Acids of Methanosphaera stadtmanae: Biosynthesis and Origin of One-Carbon Units from Acetate and Carbon Dioxide.	Miller TL, Chen X, Yan B, Bank S.	Appl Environ Microbiol	10.1128/aem.61.4.1180-1186.1995	1995
Metabolism	Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis.	Gao B, Gupta RS.	BMC Genomics	10.1186/1471-2164-8-86	2007
Genetics	Distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives.	Perry SC, Beiko RG.	Genome Biol Evol	10.1093/gbe/evq004	2010
	Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes.	Kochiwa H, Tomita M, Kanai A.	BMC Evol Biol	10.1186/1471-2148-7-128	2007
Genetics	The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection.	Arakawa K, Tomita M.	Evol Bioinform Online		2007
Metabolism	Phylogenomic reconstruction of archaeal fatty acid metabolism.	Dibrova DV, Galperin MY, Mulkidjanian AY.	Environ Microbiol	10.1111/1462-2920.12359	2014
Phylogeny	The Pfam protein families database.	Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD.	Nucleic Acids Res	10.1093/nar/gkr1065	2012
	Algorithms of ancestral gene length reconstruction.	Bolshoy A, Kirzhner VM.	Biomed Res Int	10.1155/2013/472163	2013
Genetics	Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.	Wolf YI, Makarova KS, Yutin N, Koonin EV.	Biol Direct	10.1186/1745-6150-7-46	2012
	Proteomic indicators of oxidation and hydration state in colorectal cancer.	Dick JM.	PeerJ	10.7717/peerj.2238	2016
Metabolism	A novel pathway for the biosynthesis of heme in Archaea: genome-based bioinformatic predictions and experimental evidence.	Storbeck S, Rolfes S, Raux-Deery E, Warren MJ, Jahn D, Layer G.	Archaea	10.1155/2010/175050	2010
Genetics	Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice.	Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, Barry KA, Nelson KE, Torralba M, Henrissat B, Coutinho PM, Cann IK, White BA, Fahey GC.	ISME J	10.1038/ismej.2010.162	2011
Genetics	Information theoretic perspective on genome clustering.	Veluchamy A, Mehta P, Srividhya KV, Vikram H, Govind MK, Gupta R, Aziz Bin Dukhyil A, Abdullah Alharbi R, Abdullah Aloyuni S, Hassan MM, Krishnaswamy S.	Saudi J Biol Sci	10.1016/j.sjbs.2020.12.039	2021
Genetics	Modal codon usage: assessing the typical codon usage of a genome.	Davis JJ, Olsen GJ.	Mol Biol Evol	10.1093/molbev/msp281	2010
Metabolism	Computational comparative study of tuberculosis proteomes using a model learned from signal peptide structures.	Lai JS, Cheng CW, Sung TY, Hsu WL.	PLoS One	10.1371/journal.pone.0035018	2012
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
	Archaeosome vaccine adjuvants induce strong humoral, cell-mediated, and memory responses: comparison to conventional liposomes and alum.	Krishnan L, Dicaire CJ, Patel GB, Sprott GD.	Infect Immun	10.1128/iai.68.1.54-63.2000	2000
	Functional Promiscuity of Homologues of the Bacterial ArsA ATPases.	Castillo R, Saier MH.	Int J Microbiol	10.1155/2010/187373	2010
Enzymology	Modelling the evolution of the archeal tryptophan synthase.	Merkl R.	BMC Evol Biol	10.1186/1471-2148-7-59	2007
	The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization.	Kagan J, Sharon I, Beja O, Kuhn JC.	Genome Biol	10.1186/gb-2008-9-1-r20	2008
	A study in entire chromosomes of violations of the intra-strand parity of complementary nucleotides (Chargaff's second parity rule).	Powdel BR, Satapathy SS, Kumar A, Jha PK, Buragohain AK, Borah M, Ray SK.	DNA Res	10.1093/dnares/dsp021	2009
Metabolism	Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.	Lo CC, Bonner CA, Xie G, D'Souza M, Jensen RA.	Microbiol Mol Biol Rev	10.1128/mmbr.00024-09	2009
Metabolism	Role of MurT C-Terminal Domain in the Amidation of Staphylococcus aureus Peptidoglycan.	Goncalves BV, Portela R, Lobo R, Figueiredo TA, Grilo IR, Ludovice AM, de Lencastre H, Dias JS, Sobral RG.	Antimicrob Agents Chemother	10.1128/aac.00957-19	2019
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
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

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 .
#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 .
#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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Methanosphaera stadtmanae (DSM 3091, ATCC 43021, JCM 11832)

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