Food & Mood Centre researchers have published a new study in Cell Reports Medicine looking at a food- vs. supplement-based diet and its effect on the gut microbiome. Led by Dr Melissa Lane and Dr Amelia McGuinness, the study aimed to explore whether different types of very low-energy diets (VLEDs), used for weight loss, make a difference to the gut microbiome.
The study compared two distinct diets, including:
- A food-based VLED made mostly of minimally processed whole food ingredients (including vegetables, legumes, and whole grains), supplied by Be Fit Food*, compared to;
- A supplement-based VLED made mostly of highly processed industrial ingredients (including isolated proteins and fibres, along with mixtures of food additives such as emulsifiers and sweeteners).
Both of the diets were designed to be closely matched for kilojoules, fibre and macronutrients (carbohydrates, protein and fat). 47 female participants with a high body mass index (BMI) were randomly assigned to one of these groups and followed the diet for three weeks.
What we found
We found that the food-based approach led to greater gains in gut microbial diversity, which may be an indicator of a ‘healthier’ gut microbiome, compared to the supplement-based approach. We also observed an opposing pattern: in the food-based group, gut microbiome changes moved in a potentially beneficial direction, while in the supplement-based VLED group, they moved the other way.
Both diets led to similar weight loss, suggesting that the differences we saw in the gut microbiome were likely due to the type of diet rather than energy restriction.
These findings show that even when VLEDs are designed to be closely matched for kilojoules and nutrients, the level of food processing may be important. Our study showed a food-based VLED made mostly from minimally processed whole food ingredients had different effects on the gut microbiome compared with a supplement-based VLED made mostly from highly processed industrial ingredients.
This research highlights that the gut microbiome may be shaped not only by how many kilojoules you eat or the nutrient profile of a diet, but also by whether those kilojoules and nutrients come from minimally processed whole food ingredients or from highly processed industrial ingredients.
Read the full paper here and a summary below.

*Be Fit Food provided financial support for the collection and analysis of fecal gut microbiome and biochemical samples. Investigational products used in the trial were also supplied in-kind by Be Fit Food. Be Fit Food had no role in the study design, collection, analysis, or interpretation of data; the writing of the report; or the decision to submit the paper for publication.