The microbiome is one of the most active research areas in nutrition science. The relationship between keto and gut bacteria is complex and continues to be clarified by ongoing studies.
Ketogenic diets reduce Firmicutes-to-Bacteroidetes ratio (generally considered beneficial). They also reduce populations of Bifidobacterium and Lactobacillus (probiotic bacteria that depend on fermentable fibre). They increase butyrate-producing bacteria when fibre-rich keto vegetables are consumed.
The single biggest determinant of microbiome health on keto is dietary fibre intake. High-fibre keto (avocado, leafy greens, psyllium, chia) maintains microbiome diversity. Low-fibre keto reduces it.
2025-2026 research is identifying keto-adapted microbiome signatures that differ from both standard-diet and starving microbiomes — suggesting the keto microbiome has its own functional characteristics, not simply a depleted version of the normal one.
Eat high-fibre, diverse vegetables. Include fermented foods (kefir, Greek yoghurt, kimchi, sauerkraut). Consider occasional prebiotic fibre supplementation (partially hydrolysed guar gum, inulin in small amounts). Our gluten-free keto recipes and keto main dishes feature fibre-rich vegetables prominently.