Gut health is widely recognized by health professionals and consumers alike for its importance in overall health. It plays a role in digestion and absorption, immunity, inflammation and even mental well-being. (1)
A 2025 International Food Information Council (IFIC) survey found that gut health is among the top benefits people want from their diet. (2) As people increasingly look towards food as a tool to influence wellbeing, they might be curious as to how low-carb eating impacts their gut health and function. This article will review gut microbiome basics, the research connecting low-carb eating to gut health and tips for integrating these principles into your practice.
Gut Microbiome and Diet
The gut microbiome refers to the trillions of microorganisms that live in the digestive tract. Known as the body’s “hidden organ”, a balanced microbiome is a major mediator of gut and overall health.(3) Microbes help synthesize vitamins, promote immunity and ferment dietary fiber, creating metabolites that support health throughout the body.(4,5,6)
Diet is one of the most powerful ways to balance the microbiome and achieve these benefits. It is a common misconception that low-carb diets are inherently less beneficial for the gut. However, there is a substantial body of evidence showing how low-carb diets can positively influence the microbiome and effectively help maintain gut health.
Low-Carb Diets May Positively Influence the Gut Microbiota
Research shows low-carb and keto diets can positively change the makeup of microbes in the gut, leading to more diversity.(7) A wide variety of species in the gut is important as each plays a unique role in the body and works together to support various functions. A 2024 study demonstrated that the keto diet shifted both the composition and function of the gut microbiota in children with epilepsy, leading to positive changes in four species associated with seizures.(8)
Additionally, a study published in Metabolites showed that the keto diet, in combination with the Mediterranean diet, was more beneficial for the gut microbiota profile than the Mediterranean diet alone, which tends to have a higher carbohydrate content.(9)One of the most interesting observations is that low-carbohydrate approaches tend to lead to an increase in the relative abundance of Akkermansia muciniphila, a microbe associated with improved body composition, weight loss, and improved glycemic control.(10)
Low-Carb Diets May Support Gastrointestinal Function
Low-carb and keto diets have been shown to be an effective dietary strategy for managing symptoms of gastrointestinal (GI)-related diseases. One study showed that following a very low-carb diet for 4 weeks led to relief of irritable bowel syndrome (IBS) symptoms, such as decreased abdominal pain, fewer bowel movements, more regular stool consistency and increased quality of life.(11) The very low-carb intervention helped restore indicators of intestinal health that tend to be altered by IBS, which may also explain relief.
Low-carb diets also enhance gut barrier function, which controls what passes into the bloodstream from the GI tract.(12) The keto diet may lead to more production of acid and mucus by the intestinal cells, which protects pathogens from entering and enhances immunity. Finally, when the body adapts to low-carb diets, it shifts to produce more stearate in the intestine, a microbial product that may contribute to colon cell health and tumor suppression.(13)
Low-Carb Diets May Have Neuroprotective Effects
Given the close connection between the gut and brain via the gut-brain axis, research suggests low-carb diets may also impact the nervous system through alterations of the gut microbiome. One study showed that the keto diet had positive effects on mood and brain function, which may be useful for treating depression, bipolar disorder and other mood disorders. The keto diet may also lessen the cognitive decline that is observed in neurological diseases.(3) Another study found that low-carb diets may reduce the severity and recurrence of these diseases due to the changes in microbiome composition as well as the metabolites that are produced.(14)
Areas Where More Research is Needed
Despite this strong body of evidence, there have been mixed results in recent studies. For example, a small 2024 study suggests that the keto diet may result in gut microbiome imbalance, though the clinical significance is not clear.(10) More research may be needed to fully understand the effects of a low-carb diet on long-term gut health and changes in the microbiome across different populations.
Integrating Into Practice
Supporting patients on low-carb or keto diets who want to improve their gut health should involve a tailored approach to fit each person’s unique needs and goals. When personalized, a low-carb or keto diet may support gut health as effectively as standard diets.
Recommendations to best assist these patients include:
- Focus on balanced low-carb approaches rather than carb elimination. Atkins offers 3 different evidence-based approaches (up to 20g, 40g, or 100g of net carbs per day) to offer greater flexibility and personalization.
- Emphasize filling the plate with Foundation Vegetables. These are non-starchy vegetables that are high in fiber with a low carbohydrate count, such as leafy greens, celery, asparagus, peppers, cucumbers, and cauliflower.
- Incorporate high-fiber sources of fat like nuts, seeds, and avocado. These contribute the fiber needed to maintain gut health while staying aligned with a low-carb approach.
- Include low-carb fermented foods like sauerkraut, kimchi, kefir, and full-fat yogurt. These are rich in probiotics which help balance the beneficial bacteria in the microbiome, protect the GI tract from harmful microbes, and improve digestion. Taking a probiotic supplement could also be effective.(15)