The microbiome plays a vital role in a healthy diet

Diet-related chronic diseases are now considered a global pandemic. Thus, promoting better health amongst populations necessitates curtailing faulty and deleterious dietary patterns and evidence-based recommendations.

The human gut microbiota plays a crucial part in modulating chronic diseases and the expression of the physiological effects of diet. A recent Cell Host & Microbe study discusses the current national nutritional recommendations from the viewpoint of the gut microbiota, wherein the researchers focus on evidence suggesting that the physiological effects of diet are mediated by host-microbe interactions.

Recent research has validated the hallmarks of healthy dietary patterns, such as the inclusion of vegetables, fruit, and whole grains, as well as the avoidance of processed foods. However, confusion and controversies persist. In fact, contemporary dietary recommendations barely account for the host gut-microbiome interactions with dietary patterns.

Study: Rethinking healthy eating in light of the gut microbiome. Image Credit: marilyn barbone /

Study: Rethinking healthy eating in light of the gut microbiome. Image Credit: marilyn barbone /

Similar dietary guidelines across the globe

Most national dietary guidelines proposed over the last decade consistently state that a major part of primary meals must include vegetables, fruits, and grains, with a preference for whole grains, despite their origins from diverse dietary cultures. Comparatively, animal-based or plant-based proteins constitute only a small proportion of the recommended diets.

Importantly, foods with added sugar, salt, and saturated fats are to be consumed in limited quantities, whereas processed and/or packaged foods should be avoided.

Healthy diet and the gut microbiota

Only two dietary guidelines have mentioned the gut microbiota, of which include the 2013 Dietary Guidelines for South Africa and Dietary Guidelines for Americans, 2020-25.

Whole-plant foods are strongly recommended, as they provide dietary fibers in the form of indigestible carbohydrate polymers. These fermentable fibers, which are accessible by the gut microbiota, provide growth substrates for the gut microbes. Furthermore, these fibers prevent gut-mucus depletion and bacterial invasion into the mucus layer, thus preventing inflammation and infections from occurring in these areas.

Fermentation of natural dietary fibers yields short-chain fatty acids (SCFAs) as the primary by-product, which confer various physiological benefits. These include ecological benefits to the gut microbiome, improved gut barrier function, enhanced production of satiety hormones, increased adipose tissue lipolysis, and better insulin sensitivity.

Furthermore, whole-plant foods act as bioactive compounds that bind to dietary fibers and are instrumental in bidirectional interactions with the gut microbiota. Comparatively, gut microorganisms participate in the biotransformation of phytochemicals, thereby increasing their bioavailability and absorption, as well as antioxidative and immunomodulatory effects.

Yet, whole-plant food consumption remains low in industrialized countries. Meanwhile, controversies linger regarding suggestions to reduce the consumption of processed and ultra-processed foods.

Processed foods harbor nutrients that are more readily available for digestion, easily fermentable, promote bacterial overgrowth and render an unfavorable gut microbial composition and metabolic profile. Such foods negatively influence immune and endocrine functions and do not favor commensal colonization.

These food products can also enhance epithelial encroachment, as well as promote metabolic abnormalities, low-grade inflammation, and colitis. Additionally, the high salt concentration in processed foods was found to increase proinflammatory gene expression and exacerbate colitis in animal studies.

Vegetables and fruits

Vegetables and fruit consumption provides a high diversity of plant-based dietary fibers, the intake of which prevents chronic diseases. These fibers provide a wide range of physiological benefits that are both microbiome-related and microbiome-independent.

Some vegetables improve satiety and reduce body weight, whereas others aid in improving insulin sensitivity. Overall, the gut microbiome is partly responsible for mediating the health effects of fruits and vegetables.

Plant-based protein foods

Plant-based proteins like legumes and nuts are rich in fibers and contain phytochemicals that are more bioavailable than those of grains. The gut microbiome plays a crucial role in deriving health benefits from legumes, such as decreasing weight gain and fat accumulation.

Nuts provide unsaturated fatty acids, fiber, as well as phytochemicals that influence host-microbe interactions. Increased nut consumption also benefits human health through functional components that impact the microbiome.


Fish is considered a high-quality protein as a result of its favorable fatty-acid content, as it is a primary source of naturally occurring long-chain omega-3 fatty acids. Therefore, the regular consumption of fish is associated with cardioprotective effects and improved insulin sensitivity.

Omega-3 fatty acids favorably enhance the microbiota composition and reduce white adipose tissue inflammation. The gut microbiota is instrumental in causing the inflammatory effects due to saturated fats, which can be mitigated by the omega-3 fatty acids present in fish oil. Hence, the gut microbiome is responsible for the cardioprotective benefits of polyunsaturated fatty acids.

Dietary patterns

The combination of various foods and their intake in appropriate proportions benefits health. Food interactions can also affect the gut microbiome. Thus, certain dietary patterns, such as the Mediterranean diet, can impose gut microbiome compositional and functional alterations.

The Mediterranean diet recommends a higher intake of olive oil, vegetables, fruits, legumes, nuts, and whole grains, with moderate quantities of fish, eggs, poultry, and dairy, while limiting red and processed meats. This diet, therefore, influences host-microbe interactions.

Advanced nutritional strategies

The current national dietary guidelines align with the beneficial effects of gut microbiome-host interactions on human health. Areas where considering the gut microbiome could advance nutritional strategies include:

  • Evolutionary considerations
  • Microbiome restoration strategies
  • Reformulation of processed foods
  • Targeted microbiome modulation
  • Precision nutrition
  • Microbiome discoveries to generate hypotheses for healthy eating

Understanding the underlying mechanisms and biological feasibility of the dietary-microbiome interactions in humans can inform nutritional targets and diagnostic markers that can aid in improving health.

Diet, as well as health and well-being, are strongly connected to the gut microbiome. Thus, nutritional science must target microbiome-focused outcomes for recommending adequate dietary guidelines. Future nutritional microbiological studies must also guide healthy eating patterns, which will contribute to disease prevention and management through diet.

Journal reference:
  • Armet, A. M., Deehan, E. C., O’Sullivan, A. F., et al. (2022). Rethinking healthy eating in light of the gut microbiome. Cell Host & Microbe 30(6); 764-785. doi:10.1016/j.chom.2022.04.016.
Nidhi Saha

Written by

Nidhi Saha

I am a medical content writer and editor. My interests lie in public health awareness and medical communication. I have worked as a clinical dentist and as a consultant research writer in an Indian medical publishing house. It is my constant endeavor is to update knowledge on newer treatment modalities relating to various medical fields. I have also aided in proofreading and publication of manuscripts in accredited medical journals. I like to sketch, read and listen to music in my leisure time.


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