Phage as signatures of healthy microbiomes

Abstract

Parasites are foundational to ecosystem health both as indicator species of community productivity but also as drivers of diversity. In bacterial communities, bacteriophage viruses can play such a role as they track the dynamic composition of bacterial hosts, and in the case of lytic phages, confer a growth advantage to lower abundance bacteria while adapting to more common ones. We set out to test whether viromes can be used as signatures of microbiome health using previously published results across systems. By comparing observed phage and bacterial diversity between microbiomes characterized by disturbance (so-called dysbiosis) and those considered control populations, we were able to identify some key commonalities. While just under half of studies report significant changes in viral species richness in dysbiosis, just under two thirds of studies find the viral composition to shift in dysbiosis, with specific viral taxa enrichment acting as a common signature of dysbiosis. Our analyses also suggest that the positive relationship between bacteriome and virome alpha diversity observed in health breaks down under microbiome disturbance. Overall, while specific viral signatures of dysbiosis are likely to be highly disease- and condition-specific, existing ecological theory shows clear promise in predicting and explaining microbiome health. Future data on bacteria-phage diversity relationships may provide us with much needed opportunity to diagnose, treat, and better understand the causes of dysbiosis.

Phages indirectly maintain plant pathogen defense through regulation of the commensal microbiome

“…In comparison, phages that do not directly target bacterial pathogens have received substantially less attention. However, many diseases of animals and plants are characterized by altered phage communities (14)(15)(16)(17), suggesting that they may also modulate disease risk. As with the past efforts of the microbiome field to link bacterial community composition to disease phenotypes, it can be difficult to tell from observational data alone whether an altered community is a cause, a consequence, or simply an indicator of a disease state (18,19).…”