The microbial pan-genome

TL;DR: Members of the genus Bifidobacterium include gut commensals that are particularly abundant among the microbial communities residing in the gut of healthy breast-fed infants, where their presence has been linked to many beneficial host effects.

TL;DR: This study sequenced the deep-rooted strain Angola, a virulent Pestoides isolate, and identified numerous novel genetic signatures some of which seem to be intimately associated with plague virulence, which are valuable in the development of a robust typing system critical for forensic, diagnostic, and epidemiological studies.

TL;DR: Five single-amplified genomes from the abundant SAR202 clade of dark-ocean bacterioplankton are analyzed and found they encode multiple families of paralogous enzymes involved in carbon catabolism, including several families of oxidative enzymes that the authors hypothesize participate in the degradation of cyclic alkanes.

TL;DR: It is argued that if a causative role can be demonstrated in follow-up mechanistic studies—for example, using gnotobiotic models—such functional strains have the potential to become biomarkers for diagnostics and targets for therapeutics.

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.