Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth’s climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane oxidizing archaea. Five of these MAGs represent under-sampled (e.g., Verstraetearchaeota, Methanonatronarchaeia, ANME-1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation significantly expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea (‘ Ca . Methanoliparia’). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.

The adult phenotype of mosquitoes depends on the types of bacteria encountered environmentally during development.

Listeria monocytogenes is responsible for gastroenteritis in healthy individuals and for a severe invasive disease in immunocompromised patients. Among the three identified L. monocytogenes evolutionary lineages, lineage I strains are overrepresented in epidemic listeriosis outbreaks, but the mechanisms underlying the higher virulence potential of strains of this lineage remain elusive. Here, we demonstrate that Listeriolysin S (LLS), a virulence factor only present in a subset of lineage I strains, is a bacteriocin highly expressed in the intestine of orally infected mice that alters the host intestinal microbiota and promotes intestinal colonization by L. monocytogenes, as well as deeper organ infection. To our knowledge, these results therefore identify LLS as the first bacteriocin described in L. monocytogenes and associate modulation of host microbiota by L. monocytogenes epidemic strains to increased virulence.T he gram-positive bacterium Listeria monocytogenes is a facultative intracellular pathogen that causes foodborne infections in humans and animals. Upon consumption of contaminated food, L. monocytogenes reaches the intestinal lumen, crosses the intestinal barrier, and disseminates within the host. The clinical manifestations of listeriosis vary from a mild, self-limiting gastroenteritis to severe intestinal and systemic infections, with a fatality rate estimated to 20-30% of infected individuals (1). Host gut microbiota plays a critical role in resistance against colonization by invading pathogens within the intestine (2). The mechanisms of L. monocytogenes to compete with the host microbiota to survive in the intestine remain unknown.During the last decades, the majority of Listeria studies in bacterial pathophysiology, cell biology, and immunology compared three pathogenic strains from lineage II: EGD, EGD-e, and 10403S (3). Interestingly, major listeriosis epidemics have been preferentially associated to L. monocytogenes clonal groups belonging to the evolutionary lineage I and, more specifically, to serotype 4b (4, 5), but the molecular mechanisms that contribute to the higher virulence potential of these bacterial strains have not been identified yet.Bacteriocins are bacterially synthesized proteinaceous substances that target and inhibit the growth of closely related bacteria, allowing competition in diverse ecological niches, including the digestive tract (6, 7). Production of these antimicrobial peptides is widespread among bacterial species, and such production is made possible by biosynthetic machineries present in the genome, plasmids, or conjugative transposons (7). A conserved biosynthetic gene cluster for the production of bacteriocins displaying thiazole and oxazole heterocycles was discovered in 2008 in six microbial phyla (8). These gene clusters encode a toxin precursor and all indispensable proteins for toxin maturation in a mode similar to that associated with the bacteriocin microcin B17 (8). This gene cluster in L .monocytogenes was only present in a subset of lineage I strains...