The gut microbiome could be the ‘black box’ of nutritional research

In a recent article published in the Cell journal, researchers from the University of Alberta, Canada, and University College Cork, Ireland, analyzed current nutritional guidelines for the gut microbiota.

Conclusion: Rethinking healthy eating in light of the gut microbiome. Image Credit: Kateryna Kon/Shutterstock


Food is essential to human health and to the pathogenesis of chronic non-communicable diseases at the epidemic level. The steady increase in chronic disease among non-industrialized populations converting to Western-style diets is striking testimony to the far-reaching influence of diet on human health.

Evidence-based dietary advice is essential for health promotion, given the global epidemic of diet-related chronic diseases. Although the human gut microbiota is of significant importance for the physiological consequences of diet and the genesis of chronic diseases, national dietary guidelines around the world are only beginning to take advantage of scientific advances in the microbiome sector.

Studies at the intersection of microbiome and nutrition disciplines have grown recently. Nevertheless, diet-microbiome-host relationships have received little attention in current dietary guidelines.

About the study

In this review, researchers approached current nutritional guidelines from the perspective of microbiome science, focusing on mechanistic findings that revealed host-microbe interactions as drivers of physiological impacts of diet. Scientists have narrowed their discussions of food-based dietary guidelines for health promotion and disease prevention among the general public, which is the goal of these guidelines.

The team focused on studies that showed how the gut microbiota regulates and facilitates the physiological impacts of food compounds, dietary habits and specific foods. They have used their findings to help clarify nutrition debates, create innovative nutritional advice, and provide an experimental paradigm for integrating the microbiome into nutritional research.

Interactions between gut microbiota and recommended foods

The authors found that the national dietary guidelines of many countries with varying dietary traditions exhibit a high level of consistency. These guidelines were in line with other major nutrition platforms, such as the EAT-Lancet Commission on Healthy Diets and Sustainable Food Systems and the Harvard TH Chan School of Public Health.

All of the dietary guidelines recommended whole plant-based foods like fruits, vegetables, legumes, whole grains and nuts instead of processed foods with added salt, saturated fats or sugar. Dietary fiber and phytochemicals comprise two essential components of whole plant foods.

Rapidly fermentable elements in processed foods could induce excessive growth of bacteria in the small intestine and an undesirable microbial metabolic and compositional profile. In addition, having a negative impact on the immune and endocrine systems. However, the colonic microbiota does not have access to it.

The evidence for the ability of whole grains to reduce the risk of chronic disease was strong, and the function of gut bacteria in these effects was increasingly studied. According to a study combining human research and mechanistic evaluations in mice, the microbiota may have a causal role in the health impacts of whole grains.

Several dietary standards advise frequent ingestion of plant-based protein foods because of their benefits to human and planetary health. A growing body of research indicates that the gut microbiome likely plays a role in the health benefits of legumes. Additionally, strong evidence from observational and interventional studies shows that a high intake of oily fish has a cardioprotective effect and that gut flora may be the source of these health benefits.

mediterranean diet

The Mediterranean diet incorporates many types of foods that have a favorable impact on interactions with the host. He advises fruits, vegetables, legumes, nuts, whole grains and olive oil as essential parts of the diet, a moderate consumption of eggs, poultry, fish and dairy products, and limited consumption of processed and red meats and processed foods.

Many recent microbiome studies reinforce the importance of the Mediterranean diet in dietary recommendations. Indeed, recently updated dietary guidelines advocate eating habits that reflect the Mediterranean diet, such as Dietary Approaches to Arrest Hypertension (DASH).

Food-microbe-host links on healthy eating controversies

Toxicological considerations explain the World Health Organization (WHO) or International Agency for Research on Cancer (IARC) expert group risk classification of red and processed meats, as well as existing dietary recommendations, based on probable dose-response correlations. Moreover, many mechanistic animal models highlight the potentially harmful impacts of saturated fats from milk on the homeostasis of the microbiota, reinforcing dietary recommendations to limit the consumption of high-fat dairy products.

It is uncertain whether the microbiota causally contributes to the acute metabolic consequences of low carbohydrate and low fat diets in humans. The authors noted that using microbiome-targeted techniques to improve low-carb diets would be beneficial.

Impact of gut microbiome on advancing nutritional recommendations

The team said dietary recommendations, targeted nutritional approaches and the development of food products to address chronic disease risk could benefit from considering how diet-microbiome interactions have influenced human physiology. It also laid the groundwork for initiatives to restore the microbiome. The microbiome restoration technique could theoretically be achieved with dietary synbiotics and probiotics.

It has been hypothesized that reformulation of processed foods, rather than eradication, would improve diet quality on a population scale. Such efforts will require a breakthrough in food engineering that addresses food-microbe-host interconnections.

The researchers mentioned that nutritional strategies could be used to target the microbiome and health-promoting taxa once their characteristics are recognized. Microbiome assessments were a critical part of precision nutrition methods focused on chronic disease prevention and treatment, among other individual-specific aspects, due to the highly personalized response of the gut microbiota to diet.

Experimental framework integrating the gut microbiome into nutritional investigations

Data on diet-microbiome-host relationships could improve, modify and innovate dietary recommendations. Integration of the gut microbiome into dietary recommendations should be supported by evidence of the causal and mechanistic contributions of the microbiome to the physiological impacts of diet.

The team referred to outstanding reviews that set the best practice standards for diet and microbiome studies and complemented them with a three-pillar experimental design incorporating the gut microbiome in all phases of research. nutritional. Microbiome findings to develop healthy diet hypotheses, microbiome integration in human intervention studies, and mechanistic understanding and causal inferences regarding microbiome function in diet impacts were among these pillars.


According to the authors, the convergence of fundamental concepts in the areas of nutrition and microbiome confirms current dietary recommendations. They found that the systematic integration of microbiome knowledge into nutritional studies can further boost and revolutionize healthy eating.

Overall, the study findings indicated that diet was significantly linked to the absence or presence of disease, which subsequently related to the microbiome. Diet-microbiome connections were expected to contribute to the molecular basis of dietary physiological effects, making the gut microbiome the “black box” of nutritional studies. There is a compelling evolutionary and biological rationale for the two disciplines to expand their already extensive and persistent collaborations to learn more about how to improve health through diet.

The researchers said microbiome-focused endpoints need to be integrated into all facets of nutrition science to increase the scientific basis for dietary recommendations. Additionally, nutritional microbiology research can provide comprehensive information on all elements of a healthy diet. Thus, contributing to solving the problem of prevention and control of diet-related diseases.

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