Alberta West News: Which foods most strongly alter gut microbiome composition?

Foods that most strongly alter gut microbiome composition tend to be those that are either very high in fermentable fiber and polyphenols, or very high in animal fat, animal protein, refined sugar, and certain additives such as artificial sweeteners.pmc.ncbi.nlm.nih+2

Foods that promote beneficial shifts

High‑fiber plant foods (legumes, oats, whole grains, nuts, seeds, fruits, vegetables, alliums like garlic/onion, asparagus, Jerusalem artichoke) strongly enrich fiber‑fermenting, short‑chain‑fatty‑acid (SCFA)–producing taxa such as Faecalibacterium, Roseburia, Eubacterium and Bifidobacterium.healthline+2
Polyphenol‑rich foods (berries, cocoa, coffee, tea, herbs, spices, extra‑virgin olive oil, nuts, Mediterranean‑style patterns) selectively boost SCFA producers and other beneficial bacteria while shifting metabolites toward anti‑inflammatory profiles.pmc.ncbi.nlm.nih+2

Fermented foods (yogurt, kefir, kimchi, sauerkraut, tempeh, miso, many traditional ferments) deliver live lactic acid bacteria and bioactive metabolites that can measurably change gut microbial composition and diversity, especially with regular consumption.pmc.ncbi.nlm.nih+2
Large cohort and population studies show that frequent fermented food intake associates with shifts toward butyrate‑producing bacteria and altered seasonal stability of the gut microbiota.nature+2

Diets high in red and processed meat, saturated fat and low in fiber reduce overall bacterial diversity and favor bile‑tolerant, pro‑inflammatory taxa such as Bilophila and some Bacteroides, with reduced Bifidobacterium and other beneficial groups.nature+2
Trans‑fat‑ and industrial‑fat–rich patterns further worsen metabolic and inflammatory profiles via microbiome shifts, while unsaturated fats (olive oil, nuts, fish) tend to support more favorable taxa like Bifidobacteria and Akkermansia.gutmicrobiotaforhealth+2

High‑sugar diets (glucose, fructose, sucrose) reduce diversity, increase mucus‑degrading bacteria (for example Akkermansia, Bacteroides species), and erode mucus layer integrity, promoting inflammation and barrier disruption.clevelandclinic+2
Artificial sweeteners and ultra‑processed foods (emulsifiers, additives) can markedly disturb microbial composition and function, including changes in glucose tolerance and immune signaling, even in the absence of excess calories.goldbio+2

Most powerful positive levers: large, consistent intake of diverse fibers (legumes, whole grains, vegetables, fruits, nuts/seeds), plus regular fermented and polyphenol‑rich foods.gutmicrobiotaforhealth+2
Most powerful negative levers: sustained Western‑style pattern combining red/processed meat, high saturated or trans fat, refined grains, high added sugar, artificial sweeteners and low fiber, which rapidly and reproducibly shifts the microbiome toward a pro‑inflammatory state.nature+2