Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces

Dridi, Bédis; Fardeau, Marie-Laure; Ollivier, Bernard; Raoult, Didier; Drancourt, Michel

doi:10.1099/ijs.0.033712-0

Cited by 601Anaerobic Digestion and Biogas ProductionGut microbiota and healthMicrobial Fuel Cells and Bioremediation

Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces

Dridi, Bédis, Fardeau, Marie-Laure, Ollivier, Bernard, Raoult, Didier, Drancourt, Michel·2012·International Journal of Systematic and Evolutionary Microbiology

DOI 10.1099/ijs.0.033712-0

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Abstract

During attempts to obtain novel, human-associated species of the domain Archaea , a coccoid micro-organism, designated strain B10 T , was isolated in pure culture from a sample of human faeces collected in Marseille, France. On the basis of its phenotypic characteristics and 16S rRNA and mcr A gene sequences, the novel strain was classified as a methanogenic archaeon. Cells of the strain were non-motile, Gram-staining-positive cocci that were approximately 850 nm in diameter and showed autofluorescence at 420 nm. Cells were lysed by 0.1 % (w/v) SDS. With hydrogen as the electron donor, strain B10 T produced methane by reducing methanol. The novel strain was unable to produce methane when hydrogen or methanol was the sole energy source. In an atmosphere containing CO 2 , strain B10 T could not produce methane from formate, acetate, trimethylamine, 2-butanol, 2-propanol, cyclopentanol, 2-pentanol, ethanol, 1-propanol or 2,3-butanediol. Strain B10 T grew optimally with 0.5–1.0 % (w/v) NaCl, at pH 7.6 and at 37 °C. It required tungstate-selenite for growth. The complete genome of the novel strain was sequenced; the size of the genome was estimated to be 2.05 Mb and the genomic DNA G+C content was 59.93 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, the highest sequence similarities (98.0–98.7 %) were seen between strain B10 T and several uncultured, methanogenic Archaea that had been collected from the digestive tracts of a cockroach, a chicken and mammals. In the same analysis, the non-methanogenic ‘ Candidatus Aciduliprofundum boonei’ DSM 19572 was identified as the cultured micro-organism that was most closely related to strain B10 T (83.0 % 16S rRNA gene sequence similarity). Each of the three treeing algorithms used in the analysis of 16S rRNA gene sequences indicated that strain B10 T belongs to a novel order that is distinct from the Thermoplasmatales . The novel strain also appeared to be distinct from Methanosphaera stadtmanae DSM 3091 T (72.9 % 16S rRNA gene sequence similarity), another methanogenic archaeon that was isolated from human faeces and can use methanol in the presence of hydrogen. Based on the genetic and phenotypic evidence, strain B10 T represents a novel species of a new genus for which the name Methanomassiliicoccus luminyensis gen. nov., sp. nov. is proposed. The type strain of the type species is B10 T ( = DSM 24529 T = CSUR P135 T ).

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TMA can be used for methanogenesis in the gastrointestinal tract, and this pathway is active in human intestine bacteria including Methanomassiliicoccus, Methanomethylophilus, Methanobrevibacter smithii, and Methanosphaera stadtmanae.
“TMA can be used for methanogenesis in the gastrointestinal tract; in human intestine, this pathway is active in bacteria belonging to the genera Methanomassiliicoccus and Methanomethylophilus (18,21,38) as well as in Methanobrevibacter smithii and Methanosphaera stadtmanae (41).”
From Trimethylamine N -Oxide, the Microbiome, and Heart and Kidney Disease (2017) · cites this paper as [38]
TMA can be used for methanogenesis in the gastrointestinal tract, and bacteria of the genera Methanomassiliicoccus and Methanomethylophilus have this pathway.
“TMA can be used for methanogenesis in the gastrointestinal tract, and bacteria belonging to the genera Methanomassiliicoccus and Methanomethylophilus have this pathway (18,21,38,41).”
From Trimethylamine N -Oxide, the Microbiome, and Heart and Kidney Disease (2017) · cites this paper as [38]

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Correspondence
Drancourt, M. (2016)
Self-citation
Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov.
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Self-citation
Isolement d'une nouvelle Archaea methanogène "Methanomassiliicoccus luminyensis" à partir du tube digestif humain
Dridi, B. (2011) · doi:10.70675/1702f7a9zb248z4616za4ddz67863c13ffaf
Self-citation
Methanoculleus horonobensis sp. nov., a methanogenic archaeon isolated from a deep diatomaceous shale formation
Shimizu, S., Ueno, A., Tamamura, S., Naganuma, T., & Kaneko, K. (2013) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.053520-0 · Cited by 42 · see citing works
Complete Genome Sequence of Methanomassiliicoccus luminyensis, the Largest Genome of a Human-Associated Archaea Species
Gorlas, A., Robert, C., Gimenez, G., Drancourt, M., & Raoult, D. (2012) · Journal of Bacteriology · doi:10.1128/jb.00956-12 · Cited by 75 · see citing works
Self-citation

Authors: Dridi, B., Fardeau, M.-L., Ollivier, B., Raoult, D., & Drancourt, M.
Affiliations: Centre National de la Recherche Scientifique (FR)
Aix-Marseille Université (FR)
ORCID: Fardeau, Marie-Laure
Ollivier, Bernard
Raoult, Didier
Drancourt, Michel
Venue: International Journal of Systematic and Evolutionary Microbiology
Publisher: Microbiology Society
Published: 2012-08-01
Volume: 62
Issue: Pt_8
Pages: 1902-1907
ISSN: 1466-5026 (ISSN-L)
1466-5034
DOI: 10.1099/ijs.0.033712-0
OpenAlex: W2076631370
Cited by: 596
References: 32
Citations by year: 2026: 14 · 2025: 19 · 2024: 36 · 2023: 38 · 2022: 40 · 2021: 49 · 2020: 61 · 2019: 63 · 2018: 66 · 2017: 42 · 2016: 45 · 2015: 53 · 2014: 28 · 2013: 31 · 2012: 11
FWCI: 76.70
Type: journal article
Language: en
Open access: closed
Locations: INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (publishedVersion)
PubMed (publishedVersion)
HAL (submittedVersion)
Funders: Aix-Marseille Université
Topics: Physical Sciences › Engineering › Building and Construction › Anaerobic Digestion and Biogas Production
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Physical Sciences › Environmental Science › Environmental Engineering › Microbial Fuel Cells and Bioremediation
MeSH terms: Aged, 80 and over, Archaea, Base Composition, Feces, Humans, Male, Methane, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, DNA, Archaeal, Genome, Archaeal

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Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces

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