Nonpathogenic Epsilonproteobacteria

Abstract

The Epsilonproteobacteria is a class within the phylum Proteobacteria and has been primarily recognized as a group of pathogenic microorganisms. However, nonpathogenic Epsilonproteobacteria has been increasingly of great biological importance. They represent bacteria with the highest metabolic versatility. Nonpathogenic Epsilonproteobacteria occurs dominantly in various redoxclines such as deep‐sea vents, stratified ocean, terrestrial sulfidic caves, and oil fields as both epi‐ or endosymbionts and free‐living microorganisms. Recent genome analysis has revealed that some virulence determinants and the genomic plasticity of the pathogenic Epsilonproteobacteria appear to have roots in nonpathogenic, chemoautotrophic Epsilonproteobacteria. These work advantageously for pathogenic Epsilonproteobacteria to be efficiently and persistently infectious and for nonpathogenic Epsilonproteobacteria to thrive in extreme habitats. In the genomic era, previously unrecognized evolutionary links are emerging between important human/animal pathogens and their nonpathogenic, symbiotic, chemoautotrophic relatives.

Key concepts

  • The Epsilonproteobacteria is the class within the phylum Proteobacteria and represented by important human/animal pathogens.

  • The perception of the class Epsilonproteobacteria has recently changed dramatically.

  • The Epsilonproteobacteria comprise numerous nonpathogenic bacteria with diverse ecophysiology and phylogeny.

  • Nonpathogenic Epsilonproteobacteria play key roles in biogeochemical cycles in various extreme environments on earth.

  • Nonpathogenic Epsilonproteobacteria provide new insights into the origin of animal/human pathogens.

Keywords: Epsilonproteobacteria; nonpathogenic; diversity; chemoautotroph; deep‐sea vents

Figure 1.

Phylogenetic tree of 16S rRNA gene sequences. Branch colours indicate origins of nonpathogenic Epsilonproteobacteria as follows: red, deep‐sea vents; blue, other marine habitats and green, terrestrial environments. Scale bar represents the expected number of changes per position. *, Whole‐genome sequence is available and ♯, whole genome is being sequenced.

Figure 2.

Deep‐sea vents as one of the largest reservoirs of nonpathogenic Epsilonproteobacteria. Host animals (polychaete, Paralvinella; shrimp, Alvinocaris and squat crab, Shinkaia) are shown.

Figure 3.

Conservation of gene content across proteobacterial genomes in relation to phylogenetic distance. Each dot represents a pair of species within each class of Proteobacteria (96 genomes, 1126 pairs). Conservation of gene contents was calculated by dividing the number of genes shared between two genomes by the number of genes in the smaller genome. Phylogenetic distance was calculated according to Jukes–Cantor's model using the SSU rRNA gene sequences. In addition to pairs of epsilonproteobacterial species (red), pairs of endosymbionts (green) and parasites (blue) are highlighted.

Figure 4.

16S rRNA tree, with the predicted number for protein families at each node displayed (green), and the number of families gained (upper in red) or lost (lower in blue) for each branch. Some representatives of gained or lost genes are shown in parentheses. The inference of gene content was performed using the GeneTRACE algorithm (Kunin and Ouzounis, ). Protein families were assigned using the InParanoid/MultiParanoid (Remm et al., ; O'Brien et al., ). Two Deltaproteobacteria (Geobacter sulfurreducens PCA and Desulfovibrio vulgaris Hildenborough) were used as outgroup (not shown). NLG, N‐linked glycosylation system.

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Nakagawa, Satoshi, and Takaki, Yoshihiro(Sep 2009) Nonpathogenic Epsilonproteobacteria. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0021895]