The microbial pan-genome

Abstract: Abstract Rather than a “short‐term tenant,” the tumor microbiome has been shown to play a vital role as a “permanent resident,” affecting carcinogenesis, cancer development, metastasis, and cancer therapies. As the tumor microbiome has great potential to become a target for the early diagnosis and treatment of cancer, recent research on the relevance of the tumor microbiota has attracted a wide range of attention from various scientific fields, resulting in remarkable progress that benefits from the development of interdisciplinary technologies. However, there are still a great variety of challenges in this emerging area, such as the low biomass of intratumoral bacteria and unculturable character of some microbial species. Due to the complexity of tumor microbiome research (e.g., the heterogeneity of tumor microenvironment), new methods with high spatial and temporal resolution are urgently needed. Among these developing methods, multi‐omics technologies (combinations of genomics, transcriptomics, proteomics, and metabolomics) are powerful approaches that can facilitate the understanding of the tumor microbiome on different levels of the central dogma. Therefore, multi‐omics (especially single‐cell omics) will make enormous impacts on the future studies of the interplay between microbes and tumor microenvironment. In this review, we have systematically summarized the advances in multi‐omics and their existing and potential applications in tumor microbiome research, thus providing an omics toolbox for investigators to reference in the future.

TL;DR: Comparative genomic analysis broadens the understanding of thermophilic mechanisms in the genus Porphyrobacter and may provide a useful insight in the design of thermophile enzymes for agricultural, industrial and medical applications.

TL;DR: The definition of the genomic core based on gene order conservation was demonstrated to be more robust than the simpler approach based only on gene conservation and investigated the core structures in terms of G+C content homogeneity and phylogenetic congruence.

TL;DR: Porphyromonas cangingivalis is the most prevalent canine oral bacterial species in both plaque from healthy gingiva and plaque from dogs with early periodontitis as discussed by the authors.

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.