Isolement d'une nouvelle Archaea methanogène "Methanomassiliicoccus luminyensis" à partir du tube digestif humain

Methanogenic Archaea are environmental organisms which have also been associated to mammals mucosa. In humans these microorganisms have been detected in the vaginal, intestinal and oral mucosa. These organisms are strict anaerobes and their culture conditions remains fastidious and poorly known. In fact only three methanogens have been isolated from human samples, both Methanobrevibater smithii and Methanosphaera stadtmanae from stool and Methanobrevibater oralis from dental plaque. Current knowledge on the diversity of methanogens in humans and their potential effects on human health were largely based on DNA detection methods as PCR and metagenomics. These techniques based on 16S rDNA and mcrA gene (encoding the alpha subunit of methyl coenzyme-M-reductase, a key enzyme in methanogenesis process) detection, showed that M. smithii was the most present in man and that the presence of M. stadtmanae was transient. Recently, the DNA of other methanogenic and non- methanogenic Archaea, has been detected in human feces, including sequences indicating the presence of non-cultured species belonging to potential new order of methanogens with no cultured representative. However, these studies detected M. smithii with variable prevalence in less than half of the tested individuals and no M. stadtmanae; such results does not confirm the paramount role of methanogenesis in preventing the accumulation of acids and other reaction end products during the digestion process, and can not reflect the actual amount of these two methanogens in the human digestive tract because of their specific association with the intestinal mucosa. Therefore, these studies pointed that the diversity of methanogens in humans has been underestimated suggesting the development of new molecular detection methods and cultural approaches adapted these fastidious organisms. In this work, we preset as first criteria, the detection of M. smithii in all tested individuals, therefore we developed an improved protocol for archaeal DNA extraction and detection from stool based on sequenced genomes of M. smithii and M. stadtmanae, this protocol allowed us to detect the first one DNA in 95.5% tested individuals and the second in a prevalence of 29.4%. Based on this protocol and through molecular approach based on universal amplification of methanogenic 16S rDNA, sequencing and cloning, we detected in 4% of the tested population, a sequence corresponding to a new phylotype (FJ823135) that has been previously reported and proposed as a representative of a new order of methanogens. From there, we chose one stool specimen susceptible to contain the highest amount of FJ823135 and successfully isolated Methanomassiliicoccus luminyensis B10T clone, the first cultured representative of a new order of methanogens and the fourth Archaea cultured in humans.This archaeon exhibited a similar type of metabolism to that of M. stadtmanae by oxidizing H2 and reducing methanol to methane but require tungstate-selenite, an element essential for its growth, this fact prompted us testing tungstate-selenite addition on M. stadtmanae growth and establishing that it was strongly stimulatory with a growth rate three times faster. We have thereafter studied the sensitivity of methanogens isolated from humans to antibiotics and established that they are susceptible only to molecules also effective against both Bacteria and Eucarya, in agreement with their phylogenetic location as a unique domain of life. The aim of the latter part of this work was to test the effectiveness of MALDI-TOF mass spectrometry identification of environmental and host-associated Archaea. The obtained data indicated that that MALDI-TOF-MS protein profiling is an efficient first-line step for the rapid phenotypic identification of cultured Archaea organisms including host-associated ones. [...]