The microbial pan-genome

TL;DR: Genome analysis of other epidemic ST313 isolates from Malawi and Kenya provided evidence for microevolution and clonal replacement in the field, including evidence of genome degradation, including pseudogene formation and chromosomal deletions, when compared with other S. Typhimurium genome sequences.

TL;DR: Data suggest that HGT, instead of being a “force” opposed to the emergence, persistence and global dissemination of consistent lineages, when modulated by RMSs can be the very cause of the intermediate population structures observed for the majority of pathogenic bacteria.

TL;DR: In this article , the authors describe two new members of the genus Salinibacter based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs) from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund.

Abstract: Additional file 1: Supplementary text and figures. This file (.pdf) contains Figures (and legends) S1-S3. Fig. S1 is an extension of Fig. 1 and shows the detected number of core genes with varying detection cutoffs per dataset, tool, and sequence similarity threshold. Fig. S2 and S3 provide examples of UpSet diagrams at the species (Brucella melitensis) and genus (Enterococcus spp.) level. Supplementary Text S1 details the POCP and core gene detection results for the four bacteria datasets.

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.