Epsilonproteobacteria are a metabolically versatile class that maintain different life styles including free-living as well as forming mutualistic or parasitic associations with other organisms. At deep-sea hydrothermal vents, species of this class fix inorganic carbon into organic compounds using geochemical energy sources, serving as dominant primary producers in such dark marine environments. At coastal and open ocean environments, they play important roles in the cycling of various carbon, sulfur and nitrogen containing nutrients. At human digestive systems, they can exist asymptomatically or cause diseases like peptic ulcers or gastric cancer. The global relevance of Epsilonproteobacteria has not been recognized until the past decade. For a long time, studies have been focused on the pathogenic species, such as those of the genera Helicobacter and Campylobacter. As more and more species were identified and isolated in the natural environment, today Epsilonproteobacteria is known to play important roles in the cycling of sulphidic compounds at various marine and terrestrial aquatic environments.
We ask two questions in the analyses of Epsilonproteobacteria. First, what dominates the genomic evolution of this class, the preservation of genes from common ancestry or the acquisition of genes from the environment? Second, how can the presence and absence of genes tell us about the metabolic needs of organisms in the natural environment? We performed a large-scale comparison of 39 fully sequenced genomes to examine these two questions.