Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence - between species core gene alignments

Emerging bacterial pathogens threaten global health and food security, and
so it is important to ask whether these transitions to pathogenicity have
any common features. We present a systematic study of the claim that
pathogenicity is associated with genome reduction and gene loss. We
compare broad-scale patterns across all bacteria, with detailed analyses
of Streptococcus suis, an emerging zoonotic pathogen of pigs, which has
undergone multiple transitions between disease and carriage forms. We find
that pathogenicity is consistently associated with reduced genome size
across three scales of divergence (between species within genera, and
between and within genetic clusters of S. suis). While genome reduction is
also found in mutualist and commensal bacterial endosymbionts, genome
reduction in pathogens cannot be solely attributed to the features of
their ecology that they share with these species, i.e. host restriction or
intracellularity. Moreover, other typical correlates of genome reduction
in endosymbionts (reduced metabolic capacity, reduced GC content, and the
transient expansion of non-functional elements) are not consistently
observed in pathogens. Together, our results indicate that genome
reduction is a predictive marker of pathogenicity in bacteria.