Food responses are governed by the gut microbiome, finds new study –

A study published this week reveals that the interactions of bacteria in our gut (the gut microbiome) with the food we eat differs markedly between individuals. The highly personalized nature of the gut microbiome response suggests that dietary interventions to optimize our microbiome may need to be individually tailored according to a person’s specific microbiome.

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The health and diversity of our microbiomes has long been known to affect our health. Consequently, there has been considerable research investigating the effects of diet on the bacteria that live within us. Surprisingly, cross-sectional studies have reported little difference between the impacts of different foods on bacterial populations.

The latest research investigated daily changes in human gut microbiome composition relative to dietary intake on an individual subject basis. Each of the 34 subjects kept a record of everything they ate for 17 days.

The types and quantities of bacteria present in stool samples collected over the same period were analyzed using shotgun metagenomics. The detailed analysis enabled the researchers to assess how different people’s microbiomes, as well as the enzymes and metabolic functions that they influence, were changing from day to day in response to what they ate.

The majority of subjects had detectable relationships between daily changes in the foods they consumed and daily changes in the relative abundance of species in their microbiome. However, the changes in the microbiome were not determined by the nutritional content of the subjects’ diets.

Furthermore, very few of the observed food-microbe interactions were consistent between individuals. Indeed, the data reveal that food-microbe interactions are highly personalized and related to specific foods.

A small subset of data also suggests that a varied diet is also important. Two of the study participants who consumed only a single type of meal replacement drink for the duration of the study showed microbiome variation from day to day, suggesting that a stable diet doesn’t necessarily lead to a stable microbiome.

Co-author Dan Knights, from the University of Minnesota:

The microbiome has been linked to a broad range of human conditions, including metabolic disorders, autoimmune diseases, and infections, so there is strong motivation to manipulate the microbiome with diet as a way to influence health.

This study suggests that it’s more complicated than just looking at dietary components like fibre and sugar. Much more research is needed before we can understand how the full range of nutrients in food affects how the microbiome responds to what we eat.”

Foods that have similar nutrition labels can have vastly different effects on our microbiomes. Consequently, in order to promote or suppress a particular bacterial species through a food-based intervention, the diet may need to be tailored to the specific composition of an individual’s microbiome.


Johnson AJ, et al. Cell Host and Microbe 2019;25(6):789-802.