From environment to man: genome evolution and adaptation of human opportunistic bacterial pathogens

Abstract

Environment is recognized as a huge reservoir for bacterial species and a source of human pathogens. Some environmental bacteria have an extraordinary range of activities that include promotion of plant growth or disease, breakdown of pollutants, production of original biomolecules, but also multidrug resistance and human pathogenicity. The versatility of bacterial life-style involves adaptation to various niches. Adaptation to both open environment and human specific niches is a major challenge that involves intermediate organisms allowing pre-adaptation to humans. The aim of this review is to analyze genomic features of environmental bacteria in order to explain their adaptation to human beings. The genera Pseudomonas, Aeromonas and Ochrobactrum provide valuable examples of opportunistic behavior associated to particular genomic structure and evolution. Particularly, we performed original genomic comparisons among aeromonads and between the strictly intracellular pathogens Brucella spp. and the mild opportunistic pathogens Ochrobactrum spp. We conclude that the adaptation to human could coincide with a speciation in action revealed by modifications in both genomic and population structures. This adaptation-driven speciation could be a major mechanism for the emergence of true pathogens besides the acquisition of specialized virulence factors.

Figure 1

Gene alignment of genomes of A. hydrophila, A. salmonicida and A. veronii using MAUVE multiple alignments. Colored outlined blocks surround regions of the genome sequence that aligned to part of another genome. The colored bars inside the blocks are related to the level of sequence similarities. Lines link blocks with homology between two genomes. Genome pairs from top to bottom: (A) A. hydrophila/A. salmonicida; (B) A. hydrophila/A. veronii; (C) A. salmonicida/A. veronii.

Figure 2

Gene alignment of large chromosome (ChrI) of B. suis, O. intermedium and O. anthropi using MAUVE multiple alignments. Colored outlined blocks surround regions of the genome sequence that aligned to part of another genome. The colored bars inside the blocks are related to the level of sequence similarities. Lines link blocks with homology between two genomes. Genome from top to bottom: (A) B. suis; (B) O. intermedium; and (C) O. anthropi.

Figure 3

Gene alignment of small chromosome (ChrII) of B. suis, O. intermedium and O. anthropi using MAUVE multiple alignments. Colored outlined blocks surround regions of the genome sequence that aligned to part of another genome. The colored bars inside the blocks are related to the level of sequence similarities. Lines link blocks with homology between two genomes. Genome from top to bottom: (A) B. suis; (B) O. intermedium; and (C) O. anthropi.