Name: Methanomethylovorans hollandica DSM 15978
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7053

Type strain:

Species: Methanomethylovorans hollandica

Culture col. no.: DSM 15978, NBRC 107637, DMS 1

Strain history: <- B. P. Lomans, University of Nijmegen, Department of Microbiology and Evolutionary Biology, Nijmegen, Netherlands; DMS1 <- B. P. Lomans; {1994}

NCBI tax ID(s): 867904 (strain), 101192 (species)

SI-ID 131425

DSM 15978

Special Collections

DSMZ

Section

When using BacDive for research please cite our paper

Methanomethylovorans hollandica DSM 15978 is an anaerobe, mesophilic archaeon that was isolated from anaerobic sediment of eutrophic freshwater pond.

anaerobe
mesophilic
16S sequence
Archaea
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Archaea*
	Phylum	*Methanobacteriota*
	Class	*Methanosarcinia*
	Order	*Methanosarcinales*
	Family	*Methanosarcinaceae*
	Genus	*Methanomethylovorans*
	Species	**Methanomethylovorans hollandica**
	Full Scientific Name (LPSN)	Methanomethylovorans hollandica Lomans et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #6214]

Incubation period

3-7 days

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6214]

Culture medium

ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)

[Ref.: #6214]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #6214]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6214]	Oxygen tolerance	anaerobe
[Ref.: #125439]	Oxygen tolerance	anaerobe Confidence in %90.4

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	100	8 of 8
[Ref.: #66794]	methanofuran biosynthesis	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[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]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	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]	glycolysis	76.47	13 of 17
[Ref.: #66794]	purine metabolism	75.53	71 of 94
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	methanogenesis from CO2	75	9 of 12
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	vitamin B12 metabolism	73.53	25 of 34
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	coenzyme M biosynthesis	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	lipid A biosynthesis	55.56	5 of 9
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	oxidative phosphorylation	54.95	50 of 91
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	alginate biosynthesis	50	2 of 4
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	ppGpp biosynthesis	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	non-pathway related	47.37	18 of 38
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	alanine metabolism	44.83	13 of 29
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	lysine metabolism	42.86	18 of 42
[Ref.: #66794]	citric acid cycle	42.86	6 of 14
[Ref.: #66794]	tryptophan metabolism	42.11	16 of 38
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	isoprenoid biosynthesis	34.62	9 of 26
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	propionate fermentation	30	3 of 10
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #6214]	Sample type/isolated from	anaerobic sediment of eutrophic freshwater pond
[Ref.: #6214]	Geographic location (country and/or sea, region)	Nijmegen, Dekkerswald
[Ref.: #6214]	Country	Netherlands
[Ref.: #6214]	Country ISO 3 Code	NLD
[Ref.: #6214]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#Sediment
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF120163 (>99% sequence identity) for Methanomethylovorans hollandica subclade from Microbeatlas

Aquatic Samples	368
Soil Samples	45
Animal Samples	1
Plant Samples	18
Total Samples	432

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

[Ref.: #6214]

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.: #6214]	Methanomethylovorans hollandica 16S ribosomal RNA gene, partial sequence	AF120163	1449	GenBank ENA	867904 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methanomethylovorans hollandica DSM 15978	GCA_000328665	complete	GenBank ENA	867904 tax ID	*
[Ref.: #66792]	Methanomethylovorans hollandica DSM 15978	2509601008	complete	JGI IMG/M	867904 tax ID	*
[Ref.: #66792]	Methanomethylovorans hollandica DSM 15978	867904.9	complete	PATRIC	867904 tax ID	*
[Ref.: #66792]	Methanomethylovorans hollandica DSM 15978	867904.13	plasmid	PATRIC	867904 tax ID	*

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methanomethylovorans hollandica DSM 15978 DSM 15978 NCBI: GCA_000328665.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	66.04	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	84.623	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	82.898	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	88.59	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	86.284	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	85.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanomethylovorans hollandica DSM 15978 IMG: 2509601008
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	72.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	69.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	67.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	90.4

Availability in culture collections External links

[Ref.: #6214]

Culture collection no.

DSM 15978, NBRC 107637, DMS 1

[Ref.: #76510]

SI-ID 131425

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Methanomethylovorans thermophila sp. nov., a thermophilic, methylotrophic methanogen from an anaerobic reactor fed with methanol.	Jiang B, Parshina SN, van Doesburg W, Lomans BP, Stams AJM	Int J Syst Evol Microbiol	10.1099/ijs.0.63818-0	2005	*
Phylogeny	Isolation and characterization of Methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol.	Lomans BP, Maas R, Luderer R, Op den Camp HJ, Pol A, van der Drift C, Vogels GD	Appl Environ Microbiol	10.1128/AEM.65.8.3641-3650.1999	1999	*

References

#6214

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15978

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 .

#76510

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-ID131425.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Methanomethylovorans hollandica DSM 15978 DSM 15978

Methanomethylovorans hollandica DSM 15978

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