Bacteria–Bacteriophage Coevolution in the Human Gut: Implications for Microbial Diversity and Functionality

Antagonistic coevolution (AC) between bacteria and bacteriophages plays a key role in driving and maintaining microbial diversity. Consequently, AC is predicted to affect all levels of biological organisation, from the individual to ecosystem scales. Nonetheless, we know nothing about bacteria–bacteriophage AC in perhaps the most important and clinically relevant microbial ecosystem known to humankind – the human gut microbiome. In this opinion piece I review current research on bacteria–phage AC in in vitro and natural populations of microbes. I then examine the evidence and discuss the potential role of AC in driving observed patterns of intra- and interindividual variation in the gut microbiome together with detailing the potential functional consequences of such AC-driven microbial variation for human health and disease. Genomic studies demonstrate the importance of bacteria–phage antagonistic coevolution as a key driver of molecular evolution. Although research into bacteria–phage AC in naturally occurring ecosystems is in its infancy it has been demonstrated in soil, marine, and arboreal environments and is likely to be a ubiquitous process. A large proportion of variation in gut bacterial strain diversity is linked to genes associated with phage resistance evolution. Temporal analysis of metagenomic sequence data highlights a dynamic and rapidly evolving human gut microbiome (both bacteria and phages).