Studying within-species variation has traditionally been limited to culturable bacterial
isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing …

Woese and Fox's 1977 paper on the discovery of the Archaea triggered a revolution in the
field of evolutionary biology by showing that life was divided into not only prokaryotes and …

Bacteriophages drive evolutionary change in bacterial communities by creating gene flow
networks that fuel ecological adaptions. However, the extent of viral diversity and its …

Rapid growth of genome data provides opportunities for updating microbial evolutionary
relationships, but this is challenged by the discordant evolution of individual genes. Here we …

Since the first genome-scale comparisons, it has been evident that the genomes of many
species are unbound by strict vertical descent: Large differences in gene content can occur …

INTRODUCTION Bacteria are the most diverse and abundant cellular organisms on Earth,
and in recent years environmental genomics has revealed the existence of an enormous …

Plasmids mediate the horizontal transmission of genetic information between bacteria,
facilitating their adaptation to multiple environmental conditions. An especially important …

Abstract Background The 16S rRNA gene is used extensively in bacterial phylogenetics, in
species delineation, and now widely in microbiome studies. However, the gene suffers from …

BACKGROUND Microbial communities—microbiomes—are intricately linked to human
health and critical ecosystem services. New technologies allow the rapid characterization of …

Cyanobacteria are photosynthetic prokaryotes that inhabit diverse aquatic and terrestrial
environments. However, the evolutionary mechanisms involved in the cyanobacterial habitat …