Gut microbiome may be the "black box" of nutrition research

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

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


Diet is critical to human health and the pathogenesis of epidemic-level noncommunicable chronic illnesses. The constant increase of chronic diseases among non-industrialized populations who convert to a Western-style diet is a striking witness to the substantial influence of diet on human health.

Evidence-based dietary advice is critical for health promotion, considering the global epidemic of diet-associated chronic diseases. Although human gut microbiota harbor significant relevance for the physiological consequences of diet and the genesis of chronic disease, national dietary recommendations across the globe are only beginning to take advantage of scientific advancements in the microbiome sector.

Studies at the intersection of microbiome and nutrition disciplines have expanded recently. Nonetheless, diet-microbiome-host connections have received little attention in current dietary guidelines.

About the study

In the present review, the researchers addressed current nutritional guidelines from the perspective of microbiome science, concentrating on mechanistic findings that revealed host-microbe interactions as drivers of the physiological impacts of diet. The scientists constricted their discussions on food-based dietary guidelines for health promotion and illness prevention among the common public, which is the goal of these guidelines.

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

Interactions between gut microbiota and recommended foods

The authors found that national food-based dietary guidelines from many countries with various dietary traditions have a high level of consistency. These guidelines were in accord with other major nutritional platforms, like the EAT-Lancet Commission on healthy diets and sustainable food systems and the Harvard T.H. Chan School of Public Health.

All dietary guidelines advised whole-plant foods like fruits, vegetables, legumes, whole grains, and nuts instead of processed foods with added salt, saturated fats, or sugar. Dietary fibers and phytochemicals comprise two vital components of whole-plant foods. 

The rapidly fermentable elements in processed foods might induce excessive growth of bacteria in the small intestine and an undesirable microbial metabolic and compositional profile. Further, adversely impact the immune and endocrine systems. However, the colonic microbiota does not have access to them.

The evidence for the capacity of whole grains to lower the likelihood of chronic diseases was strong, and the function of gut bacteria in these effects was being studied more and more. According to a study combining human research and mechanistic assessments in mice, the microbiota may have a causal role in the health impacts of whole grains.

Several dietary standards advise that plant-associated protein foods should be ingested frequently owing to their advantages to human and planetary health. Mounting studies indicate the gut microbiome probably has a role in the health benefits of legumes. Furthermore, solid proof from observational and intervention studies shows that high fatty fish consumption has a cardioprotective effect, and the gut flora might be mediating these health benefits.

Mediterranean diet

The Mediterranean diet integrates many food types that have a favorable impact on host interactions. It advises fruits, vegetables, legumes, nuts, whole grains, and olive oil as dietary essentials, moderate consumption of eggs, poultry, fish, and dairy products, and limited consumption of processed and red meats and processed foods.

Multiple latest microbiome studies bolster the prominence of the Mediterranean diet in dietary guidelines. Indeed, recently updated dietary guidelines advocate eating patterns that mirror the Mediterranean diet, such as the dietary approaches to stop hypertension (DASH).

Diet-microbe-host connections on controversies of eating healthy

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

It is uncertain if the microbiota contributes causally to acute metabolic consequences of low-carbohydrate and fat diets among humans. The authors noted using microbiome-targeted techniques to enhance low-carbohydrate diets will be beneficial.

Impact of gut microbiome on advancing nutritional guidelines

The team stated that dietary recommendations, focused nutritional approaches, and the development of food products to combat chronic disease risk might benefit from accounting for how diet-microbiome interactions influenced human physiology. It also laid the groundwork for initiatives to restore the microbiome. The microbiome restoration technique might be achieved theoretically with dietary synbiotics and probiotics.

Reformulation of processed foods, rather than eradication, has been hypothesized to enhance the population-wide quality of diet. Such efforts will necessitate a food engineering breakthrough that addresses diet-microbe-host interconnections.

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

Experimental framework integrating gut microbiome to nutrition investigations

Data on diet-microbiome-host relationships could improve, modify, and innovate dietary guidelines. Integrating the gut microbiome into dietary recommendations must be supported by proof of the microbiome's causal and mechanistic contributions to the physiological impacts of diet. 

The team referred to outstanding reviews that lay out best-practice standards for diet-microbiome studies and supplemented them with a three-pillared experimental design incorporating the gut microbiome within all phases of nutrition research. Microbiome discoveries to develop healthy eating hypotheses, microbiome integration into human intervention studies, and mechanistic understanding and causal inferences regarding the microbiome's function in diet impacts were among these pillars.


According to the authors, the convergence of fundamental concepts in the nutrition and microbiome sectors confirms current dietary recommendations. They discovered that systematically incorporating microbiome knowledge into nutrition studies can further boost and revolutionize healthy eating.

Overall, the study findings indicated that diet was linked significantly to the absence or presence of disease, which subsequently connected to the microbiome. Diet-microbiome connections were anticipated to contribute to the molecular underpinning of dietary physiological effects, making the gut microbiome the "black box" of nutrition 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 investigators stated that microbiome-centered endpoints must be incorporated into all facets of nutrition science to increase the scientific basis for dietary recommendations. In addition, nutritional microbiology research can provide comprehensive information on all elements of healthy eating. Thus, contributing to solving the problem of diet-linked disease prevention and control.

Journal reference:
Shanet Susan Alex

Written by

Shanet Susan Alex

Shanet Susan Alex, a medical writer, based in Kerala, India, is a Doctor of Pharmacy graduate from Kerala University of Health Sciences. Her academic background is in clinical pharmacy and research, and she is passionate about medical writing. Shanet has published papers in the International Journal of Medical Science and Current Research (IJMSCR), the International Journal of Pharmacy (IJP), and the International Journal of Medical Science and Applied Research (IJMSAR). Apart from work, she enjoys listening to music and watching movies.


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