Diet can influence the bacteria in your gut in surprising ways. Among many factors is the beneficial effect of dietary fibre through the bacteria which metabolise it, and the harmful effect of simple carbohydrates with their attendant chemicals produced by ‘bad’ microorganisms. Add to this harm the inflammatory effect of the material passing through a thus compromised gut into blood and lymph.
A possible solution? Probiotics (direct bacterial supplementation) and prebiotics (the foods which ‘good’ bacteria love) such as vegetables high in fibre, combined with avoidance of simple carbohydrates such as starch and sugar such as emphasised by a nutritionally ketogenic diet.
Source: http://journal.frontiersin.org/article/10.3389/fncel.2017.00120/full