Logo of jbacterPermissionsJournals.ASM.orgJournalJB ArticleJournal InfoAuthorsReviewers
J Bacteriol. 2012 Sep; 194(17): 4745.
PMCID: PMC3415480

Complete Genome Sequence of Methanomassiliicoccus luminyensis, the Largest Genome of a Human-Associated Archaea Species


The present study describes the complete and annotated genome sequence of Methanomassiliicoccus luminyensis strain B10 (DSM 24529T, CSUR P135), which was isolated from human feces. The 2.6-Mb genome represents the largest genome of a methanogenic euryarchaeon isolated from humans. The genome data of M. luminyensis reveal unique features and horizontal gene transfer events, which might have occurred during its adaptation and/or evolution in the human ecosystem.


Methanomassiliicoccus luminyensis strain B10 was isolated from human feces by enrichment culture studies that were conducted to isolate new human-associated Archaea species (4). The strictly anaerobic strain B10 grows optimally at 37°C, pH 7.6, with 1% NaCl, and is able to produce methane by reducing methanol with hydrogen as an electron donor.

A phylogenetic analysis using 16S rRNA gene sequences showed that strain B10 is most closely related to the nonmethanogen Aciduliprofundum boonei (4). Strain B10, only the fourth euryarchaeote to be successfully cultivated and isolated from humans (5), represents the first species of a novel genus (4).

The complete genome of M. luminyensis was sequenced with a combination of shotgun and 3-kb paired-end libraries using high-throughput 454 pyrosequencing by 454 Life Sciences (Roche, Boulogne Billancourt, France). Sequence reads were assembled using a Newbler assembler (Roche), 26 contigs were generated into one scaffold, and gaps were closed by PCR on genomic DNA. A preliminary open reading frame (ORF) prediction was conducted by automated annotation with Glimmer (http://www.cbcb.umd.edu/software/glimmer/) and RAST (2). The annotation was manually cured using BLAST and the nr database of NCBI. The CRISPRfinder (http://crispr.u-psud.fr/Server/) was used to detect and identify CRISPR repeat and spacer sequences in the genome.

The M. luminyensis genome consists of a circular chromosome of 2,637,810 bp (with a high GC content of 60.5%), which is much larger than the genomes of other methanogenic Archaea isolated from humans: Methanobrevibacter smithii (1.8 Mb) (10) and Methanosphaera stadtmanae (1.77 Mb) (6).

The genome of M. luminyensis contains, surprisingly, a single 16S-23S rRNA cluster (rarely observed for methanogenic Archaea) and two copies of 5S and 42 tRNA genes. A total of 2,613 ORFs were recovered, and most of them presumably encode proteins involved in DNA/RNA metabolism, synthesis and degradation of proteins, biosynthesis of nucleotides/amino acids/fatty acids/vitamins and cofactors, and energy metabolism.

As for M. stadtmanae, the M. luminyensis genome carries a restricted methanogenesis pathway, which could explain why M. luminyensis reduces only methanol in the presence of H2 for methane formation.

Among the proteins involved in DNA metabolism, the DNA replication machinery of M. luminyensis is strongly conserved with proteins of archaeal origin such as ORC1/CDC6, RFA, Pri-1, Pri-2, MCM, RFC, PCNA, FEN, RNase H, DNA polymerase B, and DNA polymerase D (which is specific to Euryarchaea) (3). In contrast, the repair system of M. luminyensis contains proteins of nonarchaeal origin. The genome contains several genes encoding bacterial proteins such as UvrD helicase or DinG helicase, suggesting horizontal gene transfers from Bacteria found in the gut (1).

Moreover, the M. luminyensis genome contains 3 CRISPR loci and the associated proteins (Cas), which could confer a resistance against the intrusion of mobile elements such as viruses and plasmids (9). The distribution of the CRISPR/Cas systems in Archaea genomes shows an important horizontal gene transfer from Bacteria driven by mobile elements (7, 8).

These horizontal gene acquisitions from Bacteria might have contributed to the evolution and adaptation of M. luminyensis to the host niche.

Nucleotide sequence accession numbers.

The Methanomassiliicoccus luminyensis strain B10 genome sequence has been deposited in EMBL under the accession numbers CAJE01000001 to CAJE01000026.


This work was funded by Fondation Méditerranée Infection.

We have no conflicts of interest to declare.


1. Aravind L, Walker DR, Koonin EV. 1999. Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res. 27:1223–1242 [PMC free article] [PubMed]
2. Aziz RK, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. [PMC free article] [PubMed]
3. Barry ER, Bell SD. 2006. DNA replication in the Archaea. Microbiol. Mol. Biol. Rev. 70:876–887 [PMC free article] [PubMed]
4. Dridi B, Fardeau ML, Ollivier B, Raoult D, Drancourt M. Methanomassiliicoccus luminyensis, gen. nov., sp. nov., a novel methanogenic Archaea isolated from human feces. Int. J. Syst. Evol. Microbiol., in press [PubMed]
5. Dridi B, Raoult D, Drancourt M. 2011. Archaea as emerging organisms in complex human microbiomes. Anaerobe 17:56–63 [PubMed]
6. Fricke WF, et al. 2006. The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. J. Bacteriol. 188:642–658 [PMC free article] [PubMed]
7. Garrett RA, Vestergaard G, Shah SA. 2011. Archaeal CRISPR-based immune systems: exchangeable functional modules. Trends Microbiol. 19:549–556 [PubMed]
8. Horvath P, Barrangou R. 2010. CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167–170 [PubMed]
9. Koonin EV, Marakova KS. 2009. CRISPR-Cas: an adaptative immunity system in prokaryotes. Biol. Rep. 1:95 [PMC free article] [PubMed]
10. Samuel BS, et al. 2007. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc. Natl. Acad. Sci. U. S. A. 104:10643–10648 [PMC free article] [PubMed]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)
PubReader format: click here to try


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...