Name: Methanobrevibacter filiformis RFM-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6972

Type strain:

Species: Methanobrevibacter filiformis

Strain Designation: RFM-3

Culture col. no.: DSM 11501

Strain history: <- J. R. Leadbetter, Michigan State University, Center for Microbial Ecology, E. Lansing, USA; RFM-3 <- J. R. Leadbetter {1995}

NCBI tax ID(s): 55758 (species)

SI-ID 49125

DSM 11501

Section

Methanobrevibacter filiformis RFM-3 is an anaerobe, mesophilic archaeon that was isolated from hindgut of subterranean termite, Reticulitermes flavipes.

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	*Methanobrevibacter*
	Species	**Methanobrevibacter filiformis**
	Full Scientific Name (LPSN)	Methanobrevibacter filiformis Leadbetter et al. 1998

Information on morphological and physiological properties Morphology

[Ref.: #4392]

Incubation period

3-7 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4392]

Culture medium

SPOROMUSA MEDIUM (H2/CO2) (DSMZ Medium 311a)

[Ref.: #4392]

Culture medium growth

[Ref.: #4392]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4392]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4392]			growth	30 °C

[Ref.: #4392]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4392]

Oxygen tolerance

anaerobe

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[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]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	methanofuran biosynthesis	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	coenzyme M biosynthesis	80	8 of 10
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	methanogenesis from CO2	66.67	8 of 12
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	photosynthesis	64.29	9 of 14
[Ref.: #66794]	purine metabolism	62.77	59 of 94
[Ref.: #66794]	phenylalanine metabolism	61.54	8 of 13
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	vitamin B12 metabolism	58.82	20 of 34
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	valine metabolism	55.56	5 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	peptidoglycan biosynthesis	53.33	8 of 15
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	50	4 of 8
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	glutamate and glutamine metabolism	46.43	13 of 28
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	histidine metabolism	44.83	13 of 29
[Ref.: #66794]	serine metabolism	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	lysine metabolism	42.86	18 of 42
[Ref.: #66794]	tryptophan metabolism	42.11	16 of 38
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	non-pathway related	39.47	15 of 38
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	leucine metabolism	38.46	5 of 13
[Ref.: #66794]	arginine metabolism	37.5	9 of 24
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	proline metabolism	36.36	4 of 11
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetoin degradation	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	alanine metabolism	31.03	9 of 29
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	isoprenoid biosynthesis	30.77	8 of 26
[Ref.: #66794]	tetrahydrofolate metabolism	28.57	4 of 14
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	oxidative phosphorylation	26.37	24 of 91
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	25	3 of 12
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	sulfopterin metabolism	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	acetate fermentation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	glutathione metabolism	21.43	3 of 14
[Ref.: #66794]	degradation of pentoses	21.43	6 of 28
		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.: #4392]	Sample type/isolated from	hindgut of subterranean termite, Reticulitermes flavipes
[Ref.: #4392]	Host species	Reticulitermes flavipes
[Ref.: #4392]	Geographic location (country and/or sea, region)	Massachusetts, Woods Hole
[Ref.: #4392]	Country	USA
[Ref.: #4392]	Country ISO 3 Code	USA
[Ref.: #4392]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host	#Arthropoda	#Insecta
#Host Body-Site	#Gastrointestinal tract	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence U82322 (>99% sequence identity) for Methanobrevibacter from Microbeatlas

Aquatic Samples
Soil Samples
Animal Samples	2
Plant Samples
Total Samples	2

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

[Ref.: #4392]

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.: #4392]	Methanobrevibacter filiformis 16S ribosomal RNA gene, partial sequence	U82322	1363	ENA	55758 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methanobrevibacter filiformis DSM 11501	GCA_001639265	contig	GenBank	55758 tax ID	*
[Ref.: #66792]	Methanobrevibacter filiformis DSM11501	2684622740	draft	JGI IMG/M	55758 tax ID	*
[Ref.: #66792]	Methanobrevibacter filiformis strain DSM 11501	55758.3	wgs	PATRIC	55758 tax ID	*

[Ref.: #4392]

GC-content

27.0 mol%

sequence analysis

Availability in culture collections External links

[Ref.: #4392]

Culture collection no.

DSM 11501

[Ref.: #76434]

SI-ID 49125

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft Genome Sequences of Methanobrevibacter curvatus DSM11111, Methanobrevibacter cuticularis DSM11139, Methanobrevibacter filiformis DSM11501, and Methanobrevibacter oralis DSM7256.	Poehlein A, Seedorf H	Genome Announc	10.1128/genomeA.00617-16	2016	*
Phylogeny	Methanobrevibacter filiformis sp. nov., A filamentous methanogen from termite hindguts.	Leadbetter JR, Crosby LD, Breznak JA	Arch Microbiol	10.1007/s002030050574	1998	*

References

#4392

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11501

#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 .

#76434

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-ID49125.1 )

* These data were automatically processed and therefore are not curated

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