This article is not yet fully out but certainly is intriguing: http://www.cell.com/cell/abstract/S0092-8674(15)00003-3
The title is “Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease” by Norman et al.
The basic premise is that phages may very well be knocking out beneficial bacteria, in the gut, resulting in disease.
To me what’s particularly interesting about this study, what little currently can be easily accessed, is that it actually can be viewed as an argument for the benefits of phage specificity in the guise of phage-mediated biocontrol of bacteria, i.e., phage therapy as applied clinically.
Specifically (if you will pardon the pun), when phages are employed in phage therapy, there is at best an only low potential that beneficial bacteria will be directly affected because phage host ranges tend to be quite narrow, typically at best spanning a single bacterial species and potentially some members of closely related genera. This contrasts with the typical antibiotic, which can be much less discriminatory in its impact on normal microflora, potentially resulting in bacterial superinfections.
Indeed, some antibiotics even can induce prophages, resulting in antibiotics potentially giving rise to excessive phage numbers that can impact beneficial bacteria. It is even possible for antibiotics to have an indirect impact by killing off certain bacteria that might then allow an overgrowth of beneficial bacteria which in turn could result in an achievement of so-called “winner” densities. Excessively high densities of specific bacterial types may then be followed by phage-induced reductions in the presence of these beneficial bacteria to below those levels present prior to antibiotic exposure (and then potentially overgrowth of harmful bacteria).
Sure these scenarios are complex and the latter certainly speculative. But the bottom line nonetheless is this: Some phages are bad – and we know this already since many phages carry bacterial virulence factor genes – but not all phages are bad, and those phages that are good in many or most instances probably give rise to somewhat less negative impact on the body than the majority of antibiotics.
Celebrate the diversity of phages, and their specificity!