Healthy Eating and The Gut Microbiome

Diet is central to human health and the etiology of noncommunicable chronic diseases that have reached epidemic proportions. 

An important factor of the physiological effects of diet rarely considered in establishing dietary guidelines is the human gut microbiome. Our gastrointestinal tract is colonized by a dense and complex assembly of microbiomes that contribute significantly to our metabolism and immunology. 

Virtually all diet-related chronic diseases have been linked to the microbiome, supporting its role as a mediator by which diet influences disease risk. 

A recent review performed by Armet and colleagues evaluated current national food-based dietary guidelines of different countries and aspects of healthy eating in light of the gut microbiome. They focus their research on how the gut microbiome influences and mediates the physiological effects of dietary compounds, specific foods, and dietary patterns. The study appears in the journal Cell Host & Microbiome. 

Guidelines of Different Countries

The team found that most dietary guidelines provide similar recommendations overall. For example, more than half of the diet should constitute vegetables, fruits, and grain products, with whole grains prioritized over refined grains. These foods are to be complemented by smaller portions of animal-based (fish, lean meats, poultry, eggs, and dairy products) and/or plant-based proteins (legumes, nuts). 

Also, foods high in added sugar, salt, and saturated fats are recommended by all guidelines to be limited or avoided. 

Interactions Between Foods and Gut Microbiota

Most dietary guidelines from around the world do not mention the gut microbiome. The review by Armet and colleagues focused on dietary guidelines in the context of the gut microbiome, based on human studies and animal models. 

Whole-plant foods versus processed foods

Whole-plant foods are the sole relevant, naturally occurring source of dietary fibers, which are indigestible carbohydrate polymers. Of relevance to the gut microbiome are the fermentable fibers, also referred to as microbiota-accessible carbohydrates. They have shown health benefits linked to selective effects on the microbiome, as prebiotics. 

Fiber provides growth substrates for microbes that inhibit mucus-glycan metabolism, preventing gut-mucus depletion, encroachment of bacteria into the mucus layer, and downstream inflammation, and infections. 

Another key component of whole-plant foods are phytochemicals, which are nonnutritive and bioactive compounds typically bound to dietary fibers. The majority of phytochemicals are not absorbed in the small intestine and, thus, partake in bidirectional interactions with gut microbiota. 

Despite the beneficial effects of whole-plant foods, their consumption in industrialized countries is consistently lower than what is recommended. 

Vegetables and fruits

According to dietary guidelines, the largest component of a healthy diet should be vegetables and fruits.  Fruits and vegetables provide up to 8 g of dietary fiber per serving and contain a high diversity of fibers, including pectins, inulin, cellulose, xyloglucans, and stachyose. All of these fibers elicit microbiome-independent (delayed macronutrient absorption) and microbiome-dependent (SCFA-mediated attenuation of insulin resistance) physiological effects. 

Controlled-feeding trials in humans have reported that vegetables rich in inulin increased Bifidobacterium levels, promoted satiety, and reduced body weight. 

Vegetables and fruits are also important sources of phytochemicals, including polyphenols, glucosinolates, terpenoids, phytosterols, and alkaloids. 

In one study, cranberry extract, which is rich in polyphenols, induced improvements in metabolism in mice on a high-fat high-sucrose diet that were associated with an increase in Akkermansia muciniphila, a bacteria that has beneficial effects. 

Whole Grains 

Most dietary guidelines recommend consuming whole grains over refined grains. Whole grains contain unique hemicellulose fibers, such as xylans and β-(1 → 3,1 → 4)-glucans, in addition to cellulose, resistant starches, and oligosaccharides.

Human intervention trials have shown anti-inflammatory effects of whole grains occurring in parallel to changes in gut microbiota. In healthy adults, a study by Martinez and colleages showed an enrichment of putative health-promoting organisms, such as Bifidobacterium, Roseburia faecis, and Roseburia intestinalis. 


Fish is consistently encouraged in dietary guidelines as a high-quality protein source and for its favorable fatty-acid profile. Fatty fish is one of the main naturally occurring dietary sources of long-chain omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA).

Experiments in mice demonstrated that, compared with lard (rich in saturated fats), fish oil lowered Toll-like receptor activation and white adipose tissue inflammation, which has been linked to improved insulin sensitivity.

In an RCT, a fish-derived omega-3 supplement increased Coprococcus spp. abundance that negatively correlated with triglyceride-rich lipoprotein levels. The gut microbiome is a probable mediator in the cardioprotective effects of polyunsaturated fatty acids. 

Red and processed meats

Red meat has many essential micronutrients and is an important high-quality protein source. However, most dietary sources recommend consumption in moderation, and processed meats are recommended to be avoided. 

Proteolytic fermentation by gut microbes in response to red and processed meats results in the production of potentially detrimental metabolites, such as ammonia, p-cresol, and hydrogen sulfide. This has been shown to increase intestinal permeability in mice. 

Processed meats contain additional compounds not present in lean red meat that are likely to amplify microbiome-mediated detrimental effects. Most processed meats are high in saturated fat, which stimulates hepatic bile acid secretion in the small intestine.


Our diet is strongly connected to the presence or absence of disease, and based on current evidence is also linked to the gut microbiome. 

The foundation of the physiological effects of diet could be found in the interactions between our diet and our microbiome. Multiple studies continue being published on a daily basis showing the importance of the gut microbiome and its relation with multiple diseases, including not only those affecting the gut directly, but also neurodegenerative conditions, cardiovascular disease and metabolic conditions. 

Future dietary recommendations may start including the addition of different nutrients in order to optimize our microbiome and prevent these health conditions. 


Anissa M. Armet, et al. Rethinking healthy eating in light of the gut microbiome. 2022. Cell Host & Microbiome. 

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