Different environmental factors may shape human gut microbiome variation. Although diet has a major influence on gut microbiome shifts within an individual, at population level, diet contributes little to gut microbiome variation. Although our gut microbiome might contribute to interindividual variability in response to diet, close monitoring of how temporal variation in diet alters gut microbiome composition and stability at a population level has not yet been explored.

A new study, led by Dr. Dan Knights from the University of Minnesota (USA), has found that the gut microbiome responds more to particular foods than to combinations of nutrients and that microbiome responses to diet are personalized.

The researchers studied the impact of habitual diet on the gut microbiome in 34 subjects for 17 consecutive days. Both the fecal microbiome and the participants’ diet were sampled every day through shotgun metagenomic sequencing and daily 24-hour dietary records, respectively.

Although the relative abundance of gut microbial species showed a high variation within and between individuals, functional traits tended to remain stable across individuals. In contrast, a specific group of functions related to stress response, the conversion of nitrate to nitrogen and the conversion of formate to methane showed a high interindividual variability that did not correlate with nutrient and food intake.

While dietary intake shown as food groups revealed a high level of variability across individuals, the number of macro- and micronutrient profiles remained stable for each subject across the study period. These findings allowed researchers to hypothesize that the observed changes in microbial composition and metabolism could be explained by the impact of particular microbiota-accessible carbohydrates and non-nutritive compounds that cannot be characterized with conventional nutrition databases.

With the goal of better characterizing the effects of nutrient composition on the gut microbiota, Johnson and colleagues used a tree-based dietary analysis approach built from the Food and Nutrient Database for Dietary Studies and phylogenetic methods used for comparing microbial communities.

This is a flexible tool for exploring the diversity of unique foods consumed by people for particular nutrients. In the case of fiber, for instance, studying how it affects the gut microbiome depending on food source is relevant because of the gut microbiota’s varying metabolic capacity depending on fiber type.

The authors found that within the fiber-rich food groups, fruit fiber and grain fiber from similar foods led to more similar gut microbiome profiles across participants. As in previous research, these findings highlight the importance of separately assessing the effects of fiber types found in different food groups on microbiome diversity.

On the other hand, gut microbiome responses to diet were personalized, as the same foods had different effects on people’s gut microbiomes. Daily diet-gut microbiome associations improved when considering at least 2 days of dietary records.

Proof of the personalized diet-microbiome associations is that correlations between the nine food groups—including eggs, fats, vegetables, fruits, grains, pulses, meats, milks, sweets and beverages—and gut bacteria at family and species levels varied across individuals. This implies that the gut microbiome responds differently to the same food group, whereas some food-species correlations are shared across participants.

The personalized nature of dietary patterns and bacterial species was also supported by the fact that participants’ recent dietary history and current microbiome data were able to predict changes in the gut microbiome the next day. This contrasted with the consideration of gut microbiome data alone, temporary data related to participants’ diet or another subject’s dietary features.

Overall, these findings explain why, in population-level studies, diet makes a small contribution to gut microbiome variation, even between groups of people consuming different dietary patterns.

Johnson and colleagues also explored the impact of a stable diet (in this case, meal replacement beverages) on gut microbiome variation in two subjects. It was found that a monotonous (stable) diet—even when comparing weekend diet to weekday diet—was associated with changes in the gut microbiota composition similar to those reported in other study participants. These results suggest that dietary diversity might not be always a driver of gut microbiome diversity.

On the whole, this study shows that food groups rather than specific nutrients are major drivers that explain microbiome variation across different individuals. The researchers highlight in the discussion that these findings pave the way towards predicting personalized responses through the gut microbiome and subsequently tailoring dietary advice to each individual.

A recent review of methods used to conduct precision nutrition studies discusses how the microbiome may act either as a mediator of diet on host physiology. However, it is also plausible that the basal microbiome may act as a more stable modifier of how diet affects human health. What is clear is that a better understanding of the close bi-directional relationship between diet and the human gut microbiome is crucial in moving from a “one-size-fits-all” dietary approach to an integrated and personalized approach to microbiome treatment.

For updated reading on the microbiome’s role in shaping people’s response to diet, see the following reviews published in June 2019:



Johnson AJ, Vangay P, Al-Ghalith GA, et al. Daily sampling reveals personalized diet-microbiome associations in humans. Cell Host Microbe. 2019; 25(6):789-802. doi: 10.1016/j.chom.2019.05.005