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Mind your microbes for a healthier gut


Professor Fergus Shanahan

Director of the SFI Research Centre, APC Microbiome Ireland, and Chair of the Department of Medicine at University College, Cork

How diet impacts your gut health, and how your gut health impacts your immune system, your metabolism, your internal organs – including your brain.

When we eat, we feed not only ourselves but also our microbes. Feed them or lose them; this is the simple but elegant lesson of microbiome science.

A healthy diet is required for maintenance of a healthy gut microbiota. Moreover, advances in microbiome science are challenging traditional concepts of nutrition, creating new paradigms for dietary assessment and opening new avenues of research for design of future foods. The microbiome influences the development and maturation of the immune system, host metabolism and the internal organs, including the brain. Consequently, dietary factors that shape the microbiome in health and disease and at different phases of life have become the focus of renewed attention.

Dietary diversity could be as important as the quantity and quality of your food

Traditional dietary assessments focus on quantity and quality of nutrient intake with little attention to dietary diversity. However, studies from the SFI Research Centre APC Microbiome Ireland have shown that when elderly people shift toward a monotonous diet, the microbial diversity within their gut diminishes.

This makes the elderly more susceptible to infections such as Clostridium difficile (symptoms include diarrhoea, fever, nausea, abdominal pain) and more susceptible to inflammation and frailty. Dietary diversity is therefore extremely important.

Expectant mothers should eat a varied diet

At the other end of the age spectrum, it is known that a baby acquires its microbiota from the mother, which means that the expectant mother is feeding for the next generation and more attention should be directed toward her diet in the antenatal period. Moreover, the composition of milk sugars (oligosaccharides) in breast milk versus infant formula determines which microbes are retained within the infant’s gut.

Your microbiota health is linked with obesity

Since the microbiota is a net contributor to host nutrition, it should be no surprise that the composition of an individual’s microbiota has been shown to influence the risk of developing obesity. Several lines of evidence have linked the microbiota with the risk of developing obesity and related complications, such as diabetes.

Firstly, the microbiota contributes to harvesting energy from dietary intake and regulating fat storage.

Secondly, diet-induced obesity in experimental animals is associated with changes in microbial composition in the gut.

Thirdly, transplants of human microbiota from obese individuals to germ-free mice led to obesity in recipient mice.

Finally, evidence from human-to-human transplants of microbiota from lean to overweight individuals have been associated with improved metabolic health.

More intriguingly, it appears that the composition of the microbiota can modify the severity of undernutrition. Malnourished children have an immature microbiota. Colonisation of young mice with microbiota from a malnourished child leads to stunting of growth in the recipients, whereas normal growth is achieved if mice are colonised with microbiota from healthy children.

The preventive and therapeutic implications of these findings have prompted exploration of various strategies to modify the composition of the microbiota in malnourished children and experimental data have been encouraging.

Watch what you eat for healthy metabolism

Can everyone benefit from dietary adjustment aimed at improving the composition of the gut microbiota? Increasing evidence suggests that the microbiota can be used as a biomarker or read-out to inform dietary decisions and for the optimal design of personalised nutrition. In addition, the predictive power of the microbiome has been demonstrated in recent human studies where the microbiome composition predicted metabolic responses to dietary intake.

Advances in microbiome science have additional implications for food design and safety. For example, certain food additives, such as emulsifiers, have been shown to modify the microbiota, increase the permeability of the gut, and aggravate inflammation in experimental animals. In other studies, the sugar trehalose appeared to promote preferential growth of virulent forms of Clostridium difficile.

In summary, human health is inseparable from microbiome health. Are there any take-home messages? Mind your microbes, diversify your diet, avoid sustained, highly restrictive diets, and favour natural unprocessed foods.

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