I have just finished reading the entire report including the supplement. It seems that the reason this bacteria was killed off is that the diet changed the pH balance in the gut. The report mentions "Bitter Melon" as killing the bacteria (Supplementary Figure 1. Bitter melon markedly modulated the human gut microbiota in in vitro experiment) Supplementary document, page 33. I couldn't find an exact reason for the subject taking the pre-biotics but I would suspect that it is to help re-colonize the gut with 'good' bacteria.