Diets rich in fiber, plants, and polyphenols – such as the Mediterranean diet – nourishes beneficial bacteria like Clostridium sporogenes, Faecalibacterium prausnitzii, and Akkermansia muciniphila. These microbes support a balanced gut environment and promote the production of IPA and SCFAs like butyrate. As a result, these dietary patterns are consistently linked with improved gut barrier function, lower markers of immune stress, improved metabolic signaling, and greater overall resilience. 

Polyphenol-rich foods – such as berries, green tea, and extra virgin olive oil – further reinforce this effect by selectively feeding anti-inflammatory microbes while suppressing the growth of harmful species. These compounds don’t just feed the right microbes; they also modulate microbial gene expression and boost the production of protective metabolites like SCFAs and IPA. The result is increased microbial diversity alongside enhanced vascular, metabolic, and immune function.

Likewise, diets rich in omega-3 fatty acids (i.e., fatty fish, flaxseeds) influence the gut microbiome in ways that favor SCFA and potentially IPA production. They also reduce inflammatory signaling and help restore microbial balance, contributing to systemic resilience and more efficient metabolic regulation.   

In contrast, Western-style diets – high in refined sugar, unhealthy fats, processed foods, and low in fiber – disrupt this delicate equilibrium. They reduce microbial diversity, deplete beneficial species, and encourage the growth of endotoxin-producing bacteria. This promotes sustained immune strain and shifts tryptophan metabolism away from beneficial microbial conversion (like IPA) toward the kynurenine pathway, promoteing stress-associated metabolites.

Diets low in fermentable fiber are associated with weakened gut barrier resilience, persistent immune activation, and greater metabolic strain.  Excessive alcohol intake further damages the gut lining and disrupts microbial balance. Meanwhile, chronic psychological stress raises cortisol levels, upregulating the enzyme TDO, which accelerates tryptophan degradation into KYN at the expense of health-promoting indoles, like IPA. 

Lifestyle factors beyond diet also shape microbiome function. Regular physical activity supports microbial diversity and has been shown to both increase IPA and reduce KYN levels. Sleep is another crucial factor, as poor sleep or disrupted circadian rhythms have been shown to alter gut microbial composition, increase immune stress, and impair the beneficial metabolic processing of tryptophan. These changes skew tryptophan metabolism away from health-promoting pathways and toward stress-related outputs. Mindfulness practices, nature exposure, and effective stress management strategies also preserve microbial balance. By lowering cortisol, they help maintain gut integrity and favor tryptophan metabolism along pathways that generate metabolites like IPA – supporting immune regulation and psychological resilience.  

The takeaway is clear:

Your everyday choices – in what you eat, how you move, how you sleep, and how you manage stress – directly shape whether your gut microbiota is working for or against your long-term health. Diets rich in fiber, polyphenols, and healthy fats activate microbial pathways that promote resilience, regulate inflammation, and enhance metabolic performance. The result: higher levels of health-supportive metabolites like IPA and SCFAs, a stronger gut barrier, and better overall health.