The human virome in health and disease

We sequenced the genomes of the bacteria and phage, then compared them. In many cases, we found the phage genomes integrated into the bacteria. For example, in one E. coli strain from a baby, we identified phage genes on the genetic map. When we looked at the strain with or without inducer, we could see the phage present. Similarly, when we examined virus-like particles in the baby's poop, we also found this phage. This suggests that the phage enters the baby through the strain, which harbors a lysogen that the phage induces, leading to a burst and the production of virus-like particles.

While we cannot definitively say this accounts for the entire population, we observed that as the bacteria became more abundant in the baby's poop, the virus-like particles encoded by that bacteria also increased in the stool sample. In some cases, we were able to explain up to half of the viruses present.