Name: Methanobrevibacter millerae ZA-10
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 6978

Type strain:

Species: Methanobrevibacter millerae

Strain Designation: ZA-10

Culture col. no.: DSM 16643, OCM 820

Strain 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

NCBI tax ID(s): 230361 (species)

SI-ID 404514

DSM 16643

Special Collections

DSMZ

Section

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

anaerobe
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	*Methanobrevibacter*
	Species	**Methanobrevibacter millerae**
	Full Scientific Name (LPSN)	Methanobrevibacter millerae Rea et al. 2007

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6546]

Culture medium

METHANOBACTERIUM MEDIUM (DSMZ Medium 119)

[Ref.: #6546]

Culture medium growth

[Ref.: #6546]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6546]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #6546]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6546]

Oxygen tolerance

anaerobe

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme M biosynthesis	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[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]	methanofuran biosynthesis	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	methanogenesis from CO2	75	9 of 12
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	vitamin B12 metabolism	73.53	25 of 34
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	photosynthesis	64.29	9 of 14
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	purine metabolism	61.7	58 of 94
[Ref.: #66794]	phenylalanine metabolism	61.54	8 of 13
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	glutamate and glutamine metabolism	60.71	17 of 28
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	peptidoglycan biosynthesis	53.33	8 of 15
[Ref.: #66794]	alanine metabolism	51.72	15 of 29
[Ref.: #66794]	oxidative phosphorylation	50.55	46 of 91
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	non-pathway related	47.37	18 of 38
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	histidine metabolism	44.83	13 of 29
[Ref.: #66794]	serine metabolism	44.44	4 of 9
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	degradation of sugar alcohols	43.75	7 of 16
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	citric acid cycle	42.86	6 of 14
[Ref.: #66794]	lysine metabolism	40.48	17 of 42
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	leucine metabolism	38.46	5 of 13
[Ref.: #66794]	tryptophan metabolism	36.84	14 of 38
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	tetrahydrofolate metabolism	35.71	5 of 14
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	proline metabolism	27.27	3 of 11
[Ref.: #66794]	isoprenoid biosynthesis	26.92	7 of 26
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	25	3 of 12
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	ppGpp biosynthesis	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		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.: #6546]	Sample type/isolated from	bovine rumen fluid
[Ref.: #6546]	Country	USA
[Ref.: #6546]	Country ISO 3 Code	USA
[Ref.: #6546]	Continent	North America
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #6546]

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.: #6546]	Methanobrevibacter millerae strain ZA-10 16S ribosomal RNA gene, partial sequence	AY196673	1262	GenBank ENA	230361 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methanobrevibacter millerae DSM 16643	GCA_900103415	scaffold	GenBank ENA	230361 tax ID	*
[Ref.: #66792]	Methanobrevibacter millerae DSM 16643	2593339167	draft	JGI IMG/M	230361 tax ID	*
[Ref.: #66792]	Methanobrevibacter millerae strain DSM 16643	230361.8	wgs	PATRIC	230361 tax ID	*

[Ref.: #6546]

GC-content

31-32 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Methanobrevibacter millerae DSM 16643 NCBI: GCA_900103415.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	56.547	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	86.964	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	87.204	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.703	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	76.747	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	84.208	no

Availability in culture collections External links

[Ref.: #6546]

Culture collection no.

DSM 16643, OCM 820

[Ref.: #76439]

SI-ID 404514

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#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) .

#76439

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-ID404514.1 )

* These data were automatically processed and therefore are not curated

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Methanobrevibacter millerae DSM 16643

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