The microbial pan-genome

TL;DR: In this paper , the pangenome of Lactobacillaceae was analyzed using 3,591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangENomic analysis, 2) the normalized Heap's coefficient λ was found to have an average value of 0.27 (ranging from 0.07-0.37), 3) the pANGENome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the PANGENOME for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) Lactiplantibacillus plantarum contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function.

TL;DR: A novel species, Echinicola marina, is proposed based on a deep-sea sediment isolate, characterized by a complete carotenoid biosynthetic pathway and genomic features distinct from other Echinicola species, with astaxanthin production speculated.

TL;DR: A set of 101 fully sequenced Rhodobacteraceae representatives was used to analyze the relationship between conservation of genes within this family and their distance from the origin of replication to lay the foundation for a better understanding of bacterial genome evolution and the role of replication therein.

TL;DR: Reconstruction of the evolutionary pathway from symbiotic N2-fixers to their free-living ancestors makes it possible to initiate the studies based on up-to-date genome screening technologies and aimed at the issues of genetic integration of organisms into supraspecies complexes, ratios of the macro- and microevolutionary mechanisms, and development of cooperative adaptations based on altruistic interaction between the symbiotic partners.

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.