Flexible genomic islands as drivers of genome evolution

[Display omitted] •Prokaryotic populations are composed of multiple and diverse clonal lineages.•These lineages carry different flexible gene pools, many collected in genomic islands.•The wealth of genes within a single population extends ecological performance.•Viral predation plays an important role in preserving intraspecies diversity. Natural prokaryotic populations are composed of multiple clonal lineages that are different in their core genomes in a range that varies typically between 95 and 100% nucleotide identity. Each clonal lineage also carries a complement of not shared flexible genes that can be very large. The compounded flexible genome provides polyclonal populations with enormous gene diversity that can be used to efficiently exploit resources. This has fundamental repercussions for interpreting individual bacterial genomes. They are better understood as parts rather than the whole. Multiple genomes are required to understand how the population interacts with its biotic and abiotic environment.