An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery

Parker, Michael T.

The prototypical examples of commensal viruses are phages that infect bacteria [88] . No phages are known to infect human cells and therefore their presence may be primarily innocuous. The effect of phages on the composition of the microbiome, in that they may kill or inhibit growth of some bacteria, could be considered a possible detriment or benefit depending on the situation, albeit indirect. In fact, the targeted utilization of phages to eliminate unwanted bacterial pathogens (phage therapy) was introduced in the early 1900s and has many potential benefits including, but not limited to, low toxicity, treatment of antibiotic resistant infections, and rapid discovery/generation [89] . However, concern over unknown health implications and the rise of antibiotics stalled the field, though a renaissance has been building since the 1990s [90] . Many different levels of this application exist, such as treatment of animals and plants with phages to ensure better yield as well as to kill human pathogens that may grow on or in these food sources [91] . Phages are also known to be able to stimulate and/or modulate immune action in humans at multiple levels including antibody generation, development of adaptive immune cells, and innate pattern recognition (reviewed in [88] ), and the possible applications of phages in these contexts are intriguing. In the future, sections of this group may be able to re-classified as atypically pathogenic or mutualistic if their presence can be linked to roles in specific disease phenotypes, but for now they are most appropriately classified as commensal.