Diet is the most widely studied modifiable factor for shaping gut microbiota composition and function and we are beginning to understand how isolated macronutrients and micronutrients modify the gut microbiome. As nutrients are rarely consumed in isolation, scientists are moving toward examining the ability of dietary patterns to modulate the intestinal microbiota under both physiological and pathological conditions.

Two recent reviews (here; here) update what we know based on different levels of evidence about the impact of common dietary patterns on gut microbiota composition and function.

Complex carbohydrates have the greatest influence on the human gut microbiota. As not all dietary fibers can be digested by gut microbes, the term “microbiota-accessible carbohydrate” (MAC) has been proposed for complex carbohydrates that cannot be digested by humans but which are metabolically available to gut microbes.

The amount of carbohydrates accessible to gut microbes is affected by common dietary patterns that either increase, reduce or exclude specific nutrients.

The Western diet (high in animal protein and fat, low in MACs) leads to a decreased richness and diversity of total bacteria—with a marked decrease in numbers of beneficial Bifidobacterium, Lactobacillus and Eubacterium species and an increase in Bacteroides and Enterobacteria—as compared with a plant-based diet. The use of intestinal mucus as the main source of energy by gut microbes due to compromised gut barrier integrity and reduced production of short chain fatty acids (SCFAs) is a known consequence of MAC restriction.

Beyond complex carbohydrates, proteins are an important nitrogen and carbon source for gut microbes and a diet high in protein is frequently used for weight loss in Western societies. The microbiota-specific effects of dietary patterns high in proteins and low in carbohydrates—frequently encompassed under the term Paleolithic diet—have been studied through comparison of hunter-gatherer societies and industrialized populations. Both lifestyle and the high consumption of plant-derived MACs found in tubers and the roots of plants in pre-agricultural societies hinder translation of the health benefits of this kind of diet when followed in Western societies. It should also be acknowledged that high protein consumption may generate some toxic metabolites related to diseases such as colorectal cancer.

On the other hand, the ketogenic diet (KD), with carbohydrate consumption of less than 10% of total caloric intake, is being studied for neurological disorders, weight loss, cancer, and extending longevity. The preclinical effects of KD on beneficial gut microbes such as Akkermansia muciniphila and SCFA-producing bacteria in the gut are contradictory, with an overall reduction in gut microbiota diversity. On the other hand, small studies with follow-up periods covering from 1 week to 6 months in patients with refractory epilepsy and multiple sclerosis have found that KD may restore some microbiota functions impaired by the inherent disease, but with a negative impact on the intestinal environment. These findings highlight the need for further studies exploring the diet’s long-term safety.

Regarding dietary management of functional gastrointestinal disorders, the diet low in short-chain fermentable carbohydrates and polyalcohols (known as the low-FODMAPs diet), pioneered by Peter Gibson and colleagues, is a frequent treatment for irritable bowel syndrome (IBS). The short-term reduction of FODMAPs in patients with IBS leads to gut symptom relief, which subsequently persists for between 6 and 18 months after high-FODMAP foods are reintroduced to individual tolerance.

These findings highlight that the low-FODMAP diet is not a diet for life, as it may decrease beneficial bacteria including Bifidobacterium, Faecalibacterium prausnitzii and Clostridium Cluster IV levels due to decreasing the availability of fermentable carbohydrates. FODMAP restriction should therefore be implemented in the short term, followed by reintroduction and personalization, preferably with the support of registered dietitian nutritionists.

Despite this dietary restriction approach, alternative dietary approaches for IBS are also in the pipeline. In a recent pilot proof-of-concept study, scientists showed that certain prebiotics may lead to symptom improvement maintained in the short term when compared with the low-FODMAP diet. This is likely attributable to changes in the gut microbiota. Unlike long-term dietary restrictions, following the regular Mediterranean-like diet along with a prebiotic supplement may emerge as a potential dietary approach for improving abdominal pain and bloating.

Similar regimes to the low-FODMAPs diet have also arisen and they include the specific carbohydrate diet (SCD) and the gut and psychology syndrome (GAPS) diet. However, the scientific evidence supporting their effectiveness is scarce as little is known about their ability to modify the gut microbiota and confer host health benefits.

When it comes to specific dietary components, the gluten-free diet (GFD) is a special diet followed not only by patients with celiac disease (CD) but also by individuals with gastrointestinal complaints. In the short-term, the GFD has been shown to affect the composition and activity of the gut microbiota in healthy adults (here; here). Moreover, in CD patients, the GFD over two years may also lead to shifts in the gut microbiota profile, with a decrease in Bifidobacterium and Lactobacillus and an increase in potential pathobionts from the Enterobacteriaceae family. Indeed, the GFD cannot fully restore the gut microbiota imbalances typical of CD patients, with the three-year follow-up highlighting a close relationship between gut microbiota profile and persistence of symptoms. The explanation for these findings includes the absence of fructans and a lack of a prebiotic function for gluten in the GFD.

Until now the most adequate dietary pattern for preserving the diversity of gut microbes has been shown to be the Mediterranean diet, which is generally characterized by greater intake of vegetable over animal protein. Greater adherence to the Mediterranean diet has been related with increased levels of fecal short-chain fatty acids and Lactobacillus, Bifidobacterium, Eubacteria, Bacteroides, and Prevotella along with decreases in Clostridium. Meanwhile, the diet’s beneficial impact on the gut microbiota could be explained by its capacity to improve lipid profile and inflammation.

On the whole, sufficient inclusion of a variety of plant-based foods, rather than restrictive diets that exclude entire food groups, is the key to shaping high microbiota diversity. This assumption is also supported by genus and species changes driven by vegetarian and vegan diets. Although modest differences have been found in the gut microbiome of vegan versus omnivorous subjects at diversity and richness levels, a plant-based diet allows a higher availability of MAC substrates for the gut microbiota, while also providing a high bioavailability of phytochemicals that may benefit gut health.




Gentile CL, Weir TL. The gut microbiota at the intersection of diet and human health. Science. 2018; 362(6416): 776-80. doi: 10.1126/science.aau5812.

Reddel S, Putignani L, Del Chierico F. The impact of low-FODMAPs, gluten-free, and ketogenic diets on gut microbiota modulation in pathological conditions. Nutrients. 2019; 11:373. doi: 10.3390/nu11020373.

Singh RK, Chang HW, Yan D, et al. Influence of diet on the gut microbiome and implications for human health. J Transl Med. 2017; 15(1):73. doi: 10.1186/s12967-017-1175-y.