Studies on how to influence bacteria in favour of health outcomes have been prompted by the realisation that germs are essential to human life. The consumption of dietary substances that can support the ingested organisms in terms of producing an improved health result has not yet received a joint recommendation. The purpose of this paper is to explore how health management practises utilise helpful bacteria in the form of probiotics, fermented foods, and donor faeces. Additionally, we look at the logic behind choosing healthy microbial strains and designing diets to support their growth in the gut. The most prevalent inborn mistake of amino acid metabolism, Phenylketonuria (PKU), is a condition that necessitates lifetime dietary intervention. A pilot clinical trial design is described to investigate the effects of probiotics and exercise in patients with PKU. The purpose of the example design is to highlight the significance of using omics technology to determine whether the intervention elevates neuroactive biogenic amines in the plasma, increases the abundance of Eubacterium rectale, Coprococcus eutactus, Akkermansia muciniphila, or Butyricicoccus, and increases Escherichia/Shigella in the gut, all of which are considered indicators of improved health.