Nutrients and the Gut
Nutrition plays a central role in shaping the gut microbiome determining which bacteria thrive, how diverse the microbial ecosystem is, and how microbial genes behave. The composition of an individual’s diet, whether predominantly plant-based or animal-based, can shift microbial populations and influence key metabolic and neurological pathways. These changes affect not only digestion but also mood, immunity, and long-term health outcomes.
Gut microbes help regulate appetite by influencing hormones like leptin, which signals fullness, and ghrelin, which signals hunger. They also play a role in body weight regulation. A diverse microbiome is often associated with higher levels of bacteria linked to leanness and metabolic resilience. Diets rich in fresh, whole foods support this diversity, while ultra-processed, high-fat Western diets are associated with dysbiosis, a bacteria imbalance, linked to inflammation, poor digestion, and mood disorders such as depression. Certain nutrients are especially important for maintaining a healthy gut-brain axis.
Nutrients
Omega-3 Fatty Acids
Omega-3 fatty acids play a vital role in maintaining gut health. They help strengthen the intestinal barrier, reduce gut inflammation, and support the growth of beneficial bacteria, particularly those involved in producing short-chain fatty acids (SCFAs). These SCFAs, including butyrate, acetate, and propionate, are microbial metabolites that nourish colon cells, regulate immune responses, and help maintain a balanced gut environment. See here for more information on SFCAs.
By modulating the gut microbiota, omega-3s contribute to microbial diversity and reduce the abundance of pro-inflammatory species. This shift supports better digestion, improved nutrient absorption, and enhanced resilience against dysbiosis. Omega-3s also influence bile acid metabolism and mucosal immunity, both of which are critical for maintaining gut homeostasis.
While their brain-related benefits such as regulating neurotransmitters and reducing neuroinflammation are well-documented, omega-3s exert many of these effects indirectly through the gut. Their ability to promote SCFA production reinforces the gut–brain axis, helping to regulate stress responses and mood via microbial signaling pathways.
Vitamin D
Vitamin D plays a vital role in maintaining gut health. Its receptors are distributed throughout the gastrointestinal tract, where they help regulate intestinal motility, immune signaling, and microbial balance. When vitamin D levels are low, gut transit can slow down, leading to symptoms like bloating, constipation, and discomfort.
Deficiency is also associated with a reduction in beneficial bacteria, particularly those involved in maintaining gut barrier integrity and producing anti-inflammatory compounds. This microbial shift may increase susceptibility to dysbiosis and inflammation. Additionally, vitamin D influences the synthesis of B vitamins within the gut, which are essential for energy metabolism and digestive enzyme function. Altogether, adequate vitamin D supports a stable, resilient gut environment and contributes to overall digestive wellbeing.
Zinc
Zinc plays a vital role in regulating immune responses within the gastrointestinal tract, supporting mucosal integrity, and modulating inflammatory pathways that influence microbial balance. Adequate zinc levels help maintain the gut barrier, reduce oxidative stress, and promote the growth of beneficial bacteria, all of which contribute to a stable and resilient digestive environment.
Deficiency in zinc has been linked to increased intestinal permeability and a higher risk of dysbiosis. While zinc also influences neurological function, its foundational impact on gut immunity and microbial composition makes it a critical component of digestive wellbeing.
B-Vitamins
B vitamins, particularly B6, B12, and folate, play a critical role in maintaining gut health. These nutrients support microbial metabolism, digestive enzyme activity, and the synthesis of key compounds involved in energy production and nutrient absorption. Within the gut, certain bacteria contribute to the synthesis of B vitamins, but this process can be disrupted by poor diet, inflammation, or microbial imbalance.
Low levels of B vitamins are associated with impaired gut barrier function, reduced motility, and altered microbial composition, which may contribute to symptoms like fatigue, bloating, and poor digestion.
While B vitamins are also essential for neurological function, their foundational role in supporting a stable and efficient digestive system makes them vital for overall gut resilience.
Nutrients Together
Importantly, these nutrients do not act in isolation. They interact dynamically within the gut environment to shape microbial metabolism, support barrier integrity, and regulate immune responses. By influencing which microbes thrive and how they function, nutrients like omega-3s, vitamin D, B vitamins, and zinc help maintain a balanced and resilient gut ecosystem. This microbial activity drives the production of short-chain fatty acids and other metabolites that support digestion, reduce inflammation, and reinforce gut homeostasis. They shape microbial metabolism, influence the production of neuroactive compounds like serotonin and GABA, and modulate neuroinflammatory pathways.
As research advances, there is growing interest in personalised nutrition strategies that target the microbiome to improve digestive health, prevent dysbiosis, and support whole-body wellbeing from the gut outward.
Nutrition Sources
Omega-3 Fatty Acids
Combine with fibre-rich foods such as salmon with lentils or roasted veg to support SCFA synergy.
Oily fish: Salmon, mackerel, sardines, anchovies (2–3 servings/week)
Plant-based sources: Ground flaxseeds, chia seeds, walnuts, hemp seeds
Fortified foods: Omega-3 enriched eggs or plant milks
Zinc
Soak or sprout legumes and seeds to reduce phytates and improve zinc absorption.
Animal sources: Beef, lamb, shellfish especially oysters
Plant sources: Pumpkin seeds, cashews, chickpeas, quinoa
Vitamin D
Combine with healthy fats including olive oil and avocados to enhance absorption.
Fatty fish: Trout, salmon, tuna
Egg yolks and mushrooms (especially UV-exposed)
Fortified foods: Plant milks, cereals, orange juice
Sunlight: Aim for 10–30 minutes of midday sun exposure several times per week
B Vitamins (B6, B12, Folate)
Lightly steam greens to preserve folate; combine B-rich foods with prebiotics for microbial synergy.
B6: Chickpeas, bananas, potatoes, poultry
B12: Eggs, dairy, fish, meat or fortified plant-based milks for vegans
Folate: Leafy greens, lentils, asparagus, avocado