The microbial pan-genome

TL;DR: This review summarizes the genomic studies of M. abscessus and synthesizes the current knowledge surrounding the geographically diverse dominant clones identified from patient samples to discuss the limitations of core genome comparisons and the breadth of accessory genome variation that has been observed to date.

TL;DR: Mechanisms of HGT and DNA recombination are essential for understanding bacterial evolution and pathogenesis.

Abstract: Additional file 1: Supplementary figures and tables.

TL;DR: XBASE-Orth as discussed by the authors is a system for ongoing ortholog annotation, which applies a divide-and-conquer approach and adopts a pragmatic scheme that trades accuracy for speed, leading to a significant decrease in the number of alignments that need to be performed, which translates into faster computation, making ortholog computation possible on a global scale.

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.