Methanobrevibacter millerae (DSM 16643, OCM 820, ZA-10)

Name: Methanobrevibacter millerae (DSM 16643, OCM 820, ZA-10)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6978

Type strain

Strain Designation ZA-10

Culture col. no. DSM 16643 OCM 820 ZA-10 JCM 39457

NCBI tax ID(s) 230361

Special Collections DSMZ

History <- S. Rea, CSIRO Livestock Industries, Queensland Bioscience Precinct, Brisbane, Australia; ZA-10 <- T. L. Miller, New York State Department of Health, Albany, New York, USA

Links

Methanobrevibacter millerae ZA-10 is an anaerobe archaeon that was isolated from bovine rumen fluid.

anaerobe genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 404514

JCM 39457,DSM 16643

@ref 20215

Last LPSN update 2026-02-09 11:19:21

Domain Archaea

Phylum Methanobacteriota

Class Methanobacteria

Order Methanobacteriales

Family Methanobacteriaceae

Genus Methanobrevibacter

Species Methanobrevibacter millerae

Full scientific name Methanobrevibacter millerae Rea et al. 2007

Synonyms (1)

"Methanocatella millerae"

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6546	METHANOBACTERIUM MEDIUM (DSMZ Medium 119)		Medium recipe at MediaDive	Name: METHANOBACTERIUM MEDIUM (DSMZ Medium 119) Composition: NaHCO3 3.98804 g/l Na-formate 1.99402 g/l Na-acetate 0.997009 g/l Na2S x 9 H2O 0.498504 g/l L-Cysteine HCl x H2O 0.498504 g/l KH2PO4 0.498504 g/l NH4Cl 0.398804 g/l NaCl 0.398804 g/l MgSO4 x 7 H2O 0.398804 g/l Yeast extract 0.199402 g/l CaCl2 x 2 H2O 0.0498504 g/l HCl 0.00249252 g/l FeSO4 x 7 H2O 0.00199402 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l H3BO3 5.98205e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Isobutyric acid DL-2-Methylbutyric acid Valeric acid Isovaleric acid H2SO4 Sludge Distilled water
6546	MODIFIED METHANOBACTERIUM MEDIUM (DSMZ Medium 1523)		Medium recipe at MediaDive	Name: MODIFIED METHANOBACTERIUM MEDIUM (DSMZ Medium 1523) Composition: Brain heart infusion 5.98802 g/l Proteose peptone 5.98802 g/l NaHCO3 3.99202 g/l Yeast extract 1.99601 g/l Na-formate 1.99601 g/l Na-acetate 0.998004 g/l Na2S x 9 H2O 0.499002 g/l KH2PO4 0.499002 g/l L-Cysteine HCl x H2O 0.499002 g/l MgSO4 x 7 H2O 0.399202 g/l NH4Cl 0.399202 g/l NaCl 0.399202 g/l CaCl2 x 2 H2O 0.0499002 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l Pyridoxine hydrochloride 0.000299401 g/l Thiamine-HCl x 2 H2O 0.000199601 g/l Nicotinic acid 0.000199601 g/l CoCl2 x 6 H2O 0.000189621 g/l Calcium pantothenate 9.98004e-05 g/l Vitamin B12 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l p-Aminobenzoic acid 7.98403e-05 g/l ZnCl2 6.98603e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l D-(+)-biotin 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
6546	positive	growth	37

Physiology and metabolism

Oxygen tolerance

6546

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.3

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ribulose monophosphate pathway	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	coenzyme M biosynthesis	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
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	methanofuran biosynthesis	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	palmitate biosynthesis	77.27	17 of 22
66794	vitamin B1 metabolism	76.92	10 of 13
66794	methanogenesis from CO2	75	9 of 12
66794	ketogluconate metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	vitamin B12 metabolism	73.53	25 of 34
66794	NAD metabolism	72.22	13 of 18
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	threonine metabolism	70	7 of 10
66794	valine metabolism	66.67	6 of 9
66794	acetoin degradation	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	pyrimidine metabolism	66.67	30 of 45
66794	heme metabolism	64.29	9 of 14
66794	photosynthesis	64.29	9 of 14
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	purine metabolism	61.7	58 of 94
66794	phenylalanine metabolism	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	myo-inositol biosynthesis	60	6 of 10
66794	glycine betaine biosynthesis	60	3 of 5
66794	nitrate assimilation	55.56	5 of 9
66794	d-mannose degradation	55.56	5 of 9
66794	arginine metabolism	54.17	13 of 24
66794	methionine metabolism	53.85	14 of 26
66794	peptidoglycan biosynthesis	53.33	8 of 15
66794	alanine metabolism	51.72	15 of 29
66794	oxidative phosphorylation	50.55	46 of 91
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	vitamin E metabolism	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	pantothenate biosynthesis	50	3 of 6
66794	tyrosine metabolism	50	7 of 14
66794	gluconeogenesis	50	4 of 8
66794	biotin biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	non-pathway related	47.37	18 of 38
66794	urea cycle	46.15	6 of 13
66794	histidine metabolism	44.83	13 of 29
66794	serine metabolism	44.44	4 of 9
66794	cysteine metabolism	44.44	8 of 18
66794	degradation of sugar alcohols	43.75	7 of 16
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	citric acid cycle	42.86	6 of 14
66794	lysine metabolism	40.48	17 of 42
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	leucine metabolism	38.46	5 of 13
66794	tryptophan metabolism	36.84	14 of 38
66794	pentose phosphate pathway	36.36	4 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	degradation of pentoses	35.71	10 of 28
66794	tetrahydrofolate metabolism	35.71	5 of 14
66794	cyanate degradation	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	octane oxidation	33.33	1 of 3
66794	formaldehyde oxidation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sulfate reduction	30.77	4 of 13
66794	Entner Doudoroff pathway	30	3 of 10
66794	glutathione metabolism	28.57	4 of 14
66794	mevalonate metabolism	28.57	2 of 7
66794	vitamin B6 metabolism	27.27	3 of 11
66794	proline metabolism	27.27	3 of 11
66794	isoprenoid biosynthesis	26.92	7 of 26
66794	CMP-KDO 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	degradation of aromatic, nitrogen containing compounds	25	3 of 12
66794	glycogen biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	ppGpp biosynthesis	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	polyamine pathway	21.74	5 of 23

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body-Site	#Organ	#Rumen

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
6546	bovine rumen fluid	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence AY196673 (>99% sequence identity) for Methanobrevibacter millerae from Microbeatlas

Aquatic Samples	58
Soil Samples	15
Animal Samples	2129
Plant Samples	3
Total Samples	2205

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6546	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	IMG-taxon 2593339167 annotated assembly for Methanobrevibacter millerae DSM 16643	scaffold	GCA_900103415	230361.8	2593339167	230361	65.3

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6546	Methanobrevibacter millerae strain ZA-10 16S ribosomal RNA gene, partial sequence	AY196673	1262		230361

GC content

@ref	GC-content (mol%)	Method
6546	36.5	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanobrevibacter millerae DSM 16643
NCBI: GCA_900103415

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.30	no
125439	motility	BacteriaNetⓘ	no	71.50	no
125439	gram_stain	BacteriaNetⓘ	negative	84.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	80.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methanobrevibacter millerae DSM 16643
NCBI: GCA_900103415.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	56.55	no
125438	anaerobic	anaerobicⓘ	yes	86.96	yes
125438	aerobic	aerobicⓘ	no	87.20	yes
125438	spore-forming	spore-formingⓘ	no	88.70	no
125438	thermophilic	thermophileⓘ	no	76.75	yes
125438	flagellated	motile2+ⓘ	no	84.21	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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
	Evolving understanding of rumen methanogen ecophysiology.	Khairunisa BH, Heryakusuma C, Ike K, Mukhopadhyay B, Susanti D.	Front Microbiol	10.3389/fmicb.2023.1296008	2023
	Application of Mootral^TM Reduces Methane Production by Altering the Archaea Community in the Rumen Simulation Technique.	Eger M, Graz M, Riede S, Breves G.	Front Microbiol	10.3389/fmicb.2018.02094	2018
	In vitro Evaluation of Different Feeds for Their Potential to Generate Methane and Change Methanogen Diversity.	Kim SH, Mamuad LL, Jeong CD, Choi YJ, Lee SS, Ko JY, Lee SS.	Asian-Australas J Anim Sci	10.5713/ajas.2013.13260	2013
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
	Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure.	Danielsson R, Dicksved J, Sun L, Gonda H, Muller B, Schnurer A, Bertilsson J.	Front Microbiol	10.3389/fmicb.2017.00226	2017
Genetics	The complete genome sequence of the rumen methanogen Methanobrevibacter millerae SM9.	Kelly WJ, Pacheco DM, Li D, Attwood GT, Altermann E, Leahy SC	Stand Genomic Sci	10.1186/s40793-016-0171-9	2016
Phylogeny	Methanobrevibacter millerae sp. nov. and Methanobrevibacter olleyae sp. nov., methanogens from the ovine and bovine rumen that can utilize formate for growth.	Rea S, Bowman JP, Popovski S, Pimm C, Wright AG	Int J Syst Evol Microbiol	10.1099/ijs.0.63984-0	2007

References

#6546	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16643
#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) .
#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 )
#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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Methanobrevibacter millerae (DSM 16643, OCM 820, ZA-10)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900103415

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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