Methanobrevibacter filiformis (DSM 11501, RFM-3, JCM 39454)

Name: Methanobrevibacter filiformis (DSM 11501, RFM-3, JCM 39454)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6972

Type strain

Strain Designation RFM-3

Culture col. no. DSM 11501 RFM-3 JCM 39454

NCBI tax ID(s) 55758

Special Collections DSMZ

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

Links

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

anaerobe genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 49125

JCM 39454,DSM 11501

@ref 20215

Last LPSN update 2026-05-29 08:26:32

Domain Archaea

Phylum Methanobacteriota

Class Methanobacteria

Order Methanobacteriales

Family Methanobacteriaceae

Genus Methanobrevibacter

Species Methanobrevibacter filiformis

Full scientific name Methanobrevibacter filiformis Leadbetter et al. 1998

Synonyms (1)

"Methanacia filiformis"

Morphology

Colony morphology

4392

Incubation period3-7 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4392	SPOROMUSA ACIDOVORANS MEDIUM (DSMZ Medium 311c)		Medium recipe at MediaDive	Name: SPOROMUSA ACIDOVORANS MEDIUM (DSMZ Medium 311c) Composition: D-Fructose 4.97512 g/l NaCl 2.23881 g/l Casitone 1.99005 g/l Yeast extract 1.99005 g/l Na2CO3 0.995025 g/l MgSO4 x 7 H2O 0.497512 g/l NH4Cl 0.497512 g/l K2HPO4 0.348259 g/l Na2S x 9 H2O 0.298507 g/l L-Cysteine HCl x H2O 0.298507 g/l CaCl2 x 2 H2O 0.248756 g/l KH2PO4 0.228856 g/l HCl 0.00248756 g/l FeSO4 x 7 H2O 0.00199005 g/l FeCl2 x 4 H2O 0.00149254 g/l NaOH 0.000497512 g/l Sodium resazurin 0.000497512 g/l CoCl2 x 6 H2O 0.000189055 g/l Pyridoxine hydrochloride 9.95025e-05 g/l MnCl2 x 4 H2O 9.95025e-05 g/l ZnCl2 6.96517e-05 g/l p-Aminobenzoic acid 4.97512e-05 g/l Calcium D-(+)-pantothenate 4.97512e-05 g/l Nicotinic acid 4.97512e-05 g/l Riboflavin 4.97512e-05 g/l Thiamine HCl 4.97512e-05 g/l (DL)-alpha-Lipoic acid 4.97512e-05 g/l Na2MoO4 x 2 H2O 3.58209e-05 g/l NiCl2 x 6 H2O 2.38806e-05 g/l Biotin 1.99005e-05 g/l Folic acid 1.99005e-05 g/l H3BO3 5.97015e-06 g/l Na2WO4 x 2 H2O 3.9801e-06 g/l Na2SeO3 x 5 H2O 2.98507e-06 g/l CuCl2 x 2 H2O 1.99005e-06 g/l Vitamin B12 9.95025e-07 g/l Distilled water
4392	METHANOBREVIBACTER CURVATUS MEDIUM (DSMZ Medium 734)		Medium recipe at MediaDive	Name: METHANOBREVIBACTER CURVATUS MEDIUM (DSMZ Medium 734) Composition: MOPS 2.09372 g/l Nutrient broth 1.99402 g/l NaCl 0.997009 g/l Na2CO3 0.997009 g/l Yeast extract 0.498504 g/l Casamino acids 0.498504 g/l KCl 0.498504 g/l MgCl2 x 6 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l DL-Dithiothreitol 0.159521 g/l Na2SO4 0.149551 g/l CaCl2 x 2 H2O 0.0997009 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Vitamin B12 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Calcium pantothenate 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-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 D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
4392	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
4392	anaerobe
125439	facultative anaerobe	98.88

Spore formation

@ref	Spore formation	Confidence
125439		99.438

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Arthropoda	#Insecta
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
4392	hindgut of subterranean termite, Reticulitermes flavipes	Reticulitermes flavipes	Massachusetts, Woods Hole	USA	USA	North America

Taxonmaps

69479

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

Aquatic Samples	0
Soil Samples	0
Animal Samples	2
Plant Samples	0
Total Samples	2

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4392	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	ASM163926v1 assembly for Methanobrevibacter filiformis DSM 11501	contig	GCA_001639265	55758.3	2684622740	55758	10.87

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4392	Methanobrevibacter filiformis 16S ribosomal RNA gene, partial sequence	U82322	1363		55758

GC content

@ref	GC-content (mol%)	Method
4392	27.0	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM163926v1 assembly for Methanobrevibacter filiformis DSM 11501
BV-BRC: 55758.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	98.88	no
125439	gram_stain	BacteriaNetⓘ	positive	68.13	no
125439	motility	BacteriaNetⓘ	no	68.28	no
125439	spore_formation	BacteriaNetⓘ	no	99.44	no

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 .
#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 filiformis (DSM 11501, RFM-3, JCM 39454)

Name and taxonomic classification

Morphology

Colony 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_001639265

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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