The microbial pan-genome

TL;DR: The results demonstrate that although mutation may exert genome-wide influences on codon usage acting similarly in different gene sets, selection dominates as an important force to shape biasedcodon usage as genes are present in an increased number of strains.

TL;DR: In this paper, the authors report pipelines that efficiently traverse all open-access microbial genomes and assemble non-redundant genomic information, which can be used in comparative genomic analyses.

TL;DR: This study suggests that O-antigen variation was introduced to the classical bordetellae via HGT through recombination, potentially allowing for the circulation of different Bordetella strains within the same host population.

TL;DR: Over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors are identified, suggesting substantial oceanic microbial diversity.

TL;DR: The genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal infection in humans, was generated and Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactic pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.

TL;DR: Mobile elements within genomes have driven genome evolution in diverse ways and are becoming useful tools for learning more about genome evolution and gene function.

TL;DR: The current review presents the available genomics and biological data on prophages from bacterial pathogens in an evolutionary framework to demonstrate that the chromosomes from bacteria and their viruses (bacteriophages) are coevolving.