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Background  The epsilon proteobacteria, which include many important human pathogens, are presently recognized solely on the basis of their branching in rRNA trees. No unique molecular or biochemical characteristics specific for this group are known.    Results  Comparative analyses of proteins in the genomes of  Wolinella succinogenes  DSM 1740 and  Campylobacter jejuni  RM1221 against all available sequences have identified a large number of proteins that are unique to various epsilon proteobacteria ( Campylobacterales ), but whose homologs are not detected in other organisms. Of these proteins, 49 are uniquely found in nearly all sequenced epsilon-proteobacteria (viz.  Helicobacter pylori  (26695 and J99),  H. hepaticus ,  C. jejuni  (NCTC 11168, RM1221, HB93-13, 84-25, CF93-6, 260.94, 11168 and 81-176),  C. lari, C. coli, C. upsaliensis, C. fetus ,  W. succinogenes  DSM 1740 and  Thiomicrospira denitrificans  ATCC 33889), 11 are unique for the  Wolinella  and  Helicobacter  species (i.e.  Helicobacteraceae  family) and many others are specific for either some or all of the species within the  Campylobacter  genus. The primary sequences of many of these proteins are highly conserved and provide novel resources for diagnostics and therapeutics. We also report four conserved indels (i.e. inserts or deletions) in widely distributed proteins (viz. B subunit of exinuclease ABC, phenylalanyl-tRNA synthetase, RNA polymerase β '-subunit and FtsH protein) that are specific for either all epsilon proteobacteria or different subgroups. In addition, a rare genetic event that caused fusion of the genes for the largest subunits of RNA polymerase ( rpoB  and  rpoC ) in  Wolinella  and  Helicobacter  is also described. The inter-relationships amongst  Campylobacterales  as deduced from these molecular signatures are in accordance with the phylogenetic trees based on the 16S rRNA and concatenated sequences for nine conserved proteins.    Conclusion  These molecular signatures provide novel tools for identifying and circumscribing species from the  Campylobacterales  order and its subgroups in molecular terms. Although sequence information for these signatures is presently limited to  Campylobacterales  species, it is likely that many of them will also be found in other epsilon proteobacteria. Functional studies on these proteins and conserved indels should reveal novel biochemical or physiological characteristics that are unique to these groups of epsilon proteobacteria.

Molecular signatures (unique proteins and conserved indels) that are specific for the epsilon proteobacteria (Campylobacterales)