Baseline gut microbiota composition and habitual dietary intakes are implicated in individual microbiota responses to diet

Gut BacteriaAlthough previous research has shown that both diet and medications are the primary factors involved in the modulation of both structural and functional capacity of the human gut microbiota, dietary intervention studies often do not show reliable changes in the gut microbiota from an intervention.

A review, led by Dr. Genelle Healey from the Massey Institute of Food Science and Technology at School of Food and Nutrition at the Massey University (Palmerston North, New Zealand), has concluded that interindividual variability in the gut microbiota and host responsiveness make it difficult to identify reliable gut microbiota responses to a given dietary intervention.

The review first explores the current scientific evidence supporting the relationship between the gut microbiota and human diseases. Secondly, the contribution of both baseline gut microbiota composition and habitual dietary intake on how host responds to diet is covered in further detail.

The review broadly explains the role of gut microbiota dysbiosis in human disease and what is known about gut microbiota modulation strategies for enhancing human health.

The article mentions several murine and human studies that have supported the link between dysbiotic gut microbiota and the promotion or aggravation of certain chronic diseases-such as obesity, type 2 diabetes mellitus, inflammatory bowel disease, and colorectal cancer. However, the authors emphasized that uncertainty remains around whether dysbiosis is a cause or consequence of these diseases. Furthermore, a dysbiotic gut microbiota may be the result of people’s dietary patterns and commonly-prescribed medications. Even if the gut microbiota is involved in their pathogenesis, to what extent novel microbiota-based therapeutic strategies have the potential to reduce disease incidence and severity remains unknown.

Despite thess limitations, it is noted that the gut microbiota is involved in human disease and diet is considered one of the main contributors to the composition, diversity, and metabolic activity of commensal microbes that reside within the gastrointestinal tract. Based on the fact that habitual dietary intakes have a relevant impact on the composition of the gut microbiota, the review then shows several human observational and dietary intervention studies that have been conducted to explore to what extent diet -focusing on dietary fibre-associated changes in the functional capacity of the gut microbiota- could be used to modulate the gut microbiota to decrease disease risk.

Few human studies have demonstrated what influence diet can have on the entire microbial community. However, those studies that have demonstrated a beneficial role of plant-based dietary substrates in the structure and functional capacity of the gut microbiota have also shown that gut microbiota modifications are also related to improvements in host health outcomes such as immune and inflammatory markers and post-oral glucose tolerance test glycemia.

Finally, the review focuses on response of gut microbiota and host to dietary interventions. Some human intervention studies in healthy subjects, overweight or obese individuals or patients with irritable bowel syndrome have demonstrated that baseline gut microbiota composition and habitual dietary intakes are factors involved in gut microbiota responses to the diet. However, a limited number of studies have found no link between responsiveness and baseline gut microbiota composition or dietary pattern. The relevance of baseline microbiota may be related to heterogeneity in participant characteristics -different external factors including age, sex, antibiotics, and disease- and the differing dietary assessment methods and gut microbial analysis methods used. Besides this, it has been suggested that individualized gut microbiota resilience may play a more important role in gut microbiota response than dietary change itself. Further studies that determine what factors are involved in individualized responsiveness are needed in order to better design personalized gut microbiota-targeted interventions.

In an interview with GMFH editors, Dr. Genelle Healey explained how baseline gut microbiota may depend on habitual dietary patterns: “(…) if people have very distinctive diets their baseline gut microbiota composition will be quite distinctive as well. And some studies have shown maybe it’s not the makeup of the gut microbiota that’s distinctive but it’s how they function. So whether they can actually utilize the substrates that you make available to them or not, might depend on the substrates that you’re giving them on a day to day basis”.

On the whole, these results show that high inter-individual variability in gut microbiota and host responsiveness makes it hard to predict the impact of specific dietary interventions on both gut microbiota and host response. Both individualized gut microbiota and host responsiveness have the potential to influence study results and affect reproducibility among studies. Therefore, taking into account both baseline gut microbiota composition and habitual dietary intake could better establish successful gut microbiota modulation strategies.

According to Dr. Healey: “There’s some preliminary evidence to suggest that things like baseline gut microbiota composition and habitual diet actually should be considered by researchers when recruiting their participants, and/or when they’re analysing the data that they generate from dietary intervention studies. This might help ensure that the true effectiveness or efficacy of a dietary intervention is determined”.



Healey GR, Murphy R, Brough L, Butts CA, Coad J. Interindividual variability in gut microbiota and host response to dietary interventions. Nutr Rev. 2017; 75(12):1059-80. doi: 10.1093/nutrit/nux062.

Andreu Prados
Andreu Prados
Andreu Prados holds a Bachelor of Science Degree in Pharmacy & Human Nutrition and Dietetics. Science writer specialised in gut microbiota and probiotics, working also as lecturer and consultant in nutrition and healthcare. Follow Andreu on Twitter @andreuprados