Methanobrevibacter cuticularis (DSM 11139, RFM-1, JCM 39453)

Name: Methanobrevibacter cuticularis (DSM 11139, RFM-1, JCM 39453)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6971

Type strain

Strain Designation RFM-1

Culture col. no. DSM 11139 RFM-1 JCM 39453

NCBI tax ID(s) 47311

Special Collections DSMZ

Links

Methanobrevibacter cuticularis RFM-1 is an anaerobe, mesophilic prokaryote that was isolated from hindgut of termite Reticulitermes flavipes.

anaerobe mesophilic genome sequence

Name and taxonomic classification

SI-ID 49040

JCM 39453,DSM 11139

@ref 20215

Last LPSN update 2025-12-16 09:48:27

Domain Methanobacteriati

Phylum Methanobacteriota

Class Methanobacteria

Order Methanobacteriales

Family Methanobacteriaceae

Genus Methanobrevibacter

Species Methanobrevibacter cuticularis

Full scientific name Methanobrevibacter cuticularis Leadbetter and Breznak 1997

Synonyms (1)

"Methanobaculum cuticularis"

Morphology

Colony morphology

4219

Incubation period3-7 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4219	METHANOBREVIBACTER CUTICULARIS MEDIUM (DSMZ Medium 734a)		Medium recipe at MediaDive	Name: METHANOBREVIBACTER CUTICULARIS MEDIUM (DSMZ Medium 734a) Composition: MOPS 2.1 g/l Na2CO3 2.0 g/l NaCl 1.0 g/l Casamino acids 0.5 g/l KCl 0.5 g/l Yeast extract 0.5 g/l MgCl2 x 6 H2O 0.4 g/l NH4Cl 0.3 g/l KH2PO4 0.2 g/l DL-Dithiothreitol 0.16 g/l Na2SO4 0.15 g/l CaCl2 x 2 H2O 0.1 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l NaOH 0.0005 g/l Sodium resazurin 0.0005 g/l Pyridoxine hydrochloride 0.0003 g/l Nicotinic acid 0.0002 g/l Thiamine-HCl x 2 H2O 0.0002 g/l CoCl2 x 6 H2O 0.00019 g/l Calcium pantothenate 0.0001 g/l Vitamin B12 0.0001 g/l MnCl2 x 4 H2O 0.0001 g/l p-Aminobenzoic acid 8e-05 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l D-(+)-biotin 2e-05 g/l H3BO3 6e-06 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Rumen fluid Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
4219	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
4219	anaerobe
125439	facultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		94.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	formaldehyde oxidation	100	3 of 3
66794	ribulose monophosphate pathway	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ethanol fermentation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	methanofuran biosynthesis	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	coenzyme M biosynthesis	80	8 of 10
66794	glycine betaine biosynthesis	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	vitamin B12 metabolism	79.41	27 of 34
66794	valine metabolism	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	palmitate biosynthesis	77.27	17 of 22
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	threonine metabolism	70	7 of 10
66794	d-mannose degradation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	acetoin degradation	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	methanogenesis from CO2	66.67	8 of 12
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	photosynthesis	64.29	9 of 14
66794	purine metabolism	63.83	60 of 94
66794	vitamin B6 metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	vitamin B1 metabolism	61.54	8 of 13
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	myo-inositol biosynthesis	60	6 of 10
66794	cellulose degradation	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	glycolysis	58.82	10 of 17
66794	citric acid cycle	57.14	8 of 14
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	nitrate assimilation	55.56	5 of 9
66794	lipid metabolism	54.84	17 of 31
66794	peptidoglycan biosynthesis	53.33	8 of 15
66794	histidine metabolism	51.72	15 of 29
66794	heme metabolism	50	7 of 14
66794	C4 and CAM-carbon fixation	50	4 of 8
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	gluconeogenesis	50	4 of 8
66794	selenocysteine biosynthesis	50	3 of 6
66794	tyrosine metabolism	50	7 of 14
66794	ketogluconate metabolism	50	4 of 8
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	arginine metabolism	50	12 of 24
66794	propionate fermentation	50	5 of 10
66794	tryptophan metabolism	47.37	18 of 38
66794	leucine metabolism	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	non-pathway related	44.74	17 of 38
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	serine metabolism	44.44	4 of 9
66794	degradation of sugar alcohols	43.75	7 of 16
66794	propanol degradation	42.86	3 of 7
66794	lysine metabolism	42.86	18 of 42
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	O-antigen biosynthesis	40	2 of 5
66794	starch degradation	40	4 of 10
66794	glycine metabolism	40	4 of 10
66794	degradation of hexoses	38.89	7 of 18
66794	urea cycle	38.46	5 of 13
66794	alanine metabolism	37.93	11 of 29
66794	pentose phosphate pathway	36.36	4 of 11
66794	isoprenoid biosynthesis	34.62	9 of 26
66794	octane oxidation	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of pentoses	32.14	9 of 28
66794	sulfate reduction	30.77	4 of 13
66794	tetrahydrofolate metabolism	28.57	4 of 14
66794	oxidative phosphorylation	28.57	26 of 91
66794	mevalonate metabolism	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	polyamine pathway	26.09	6 of 23
66794	catecholamine biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	alginate biosynthesis	25	1 of 4
66794	allantoin degradation	22.22	2 of 9

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
4219	hindgut of termite Reticulitermes flavipes	Reticulitermes flavipes	Michigan, Dansville	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4219	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	ASM163928v1 assembly for Methanobrevibacter cuticularis DSM 11139	contig	GCA_001639285	47311.3	2684622743	47311	36.57

Genome browser: GCA_001639285

GC content

@ref	GC-content (mol%)	Method
4219	26.8	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanobrevibacter cuticularis DSM 11139
NCBI: GCA_001639285

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.50	no
125439	motility	BacteriaNetⓘ	no	63.00	no
125439	gram_stain	BacteriaNetⓘ	negative	83.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	93.80	no

Literature

Title	Authors	Journal	DOI	Year
A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution.	Grau-Bove X, Navarrete C, Chiva C, Pribasnig T, Anto M, Torruella G, Galindo LJ, Lang BF, Moreira D, Lopez-Garcia P, Ruiz-Trillo I, Schleper C, Sabido E, Sebe-Pedros A.	Nat Ecol Evol	10.1038/s41559-022-01771-6	2022
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
Physiological ecology of Methanobrevibacter cuticularis sp. nov. and Methanobrevibacter curvatus sp. nov., isolated from the hindgut of the termite Reticulitermes flavipes.	Leadbetter JR, Breznak JA	Appl Environ Microbiol	10.1128/aem.62.10.3620-3631.1996	1996

References

#4219	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11139
#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 )
#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 cuticularis (DSM 11139, RFM-1, JCM 39453)

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

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001639285

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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