Restricted diet triggers drop in microbial diversity without convergence

How much can six days of eating just oats, milk, and water change your gut microbiome? 

According to a recent exploratory study published in eGastroenterology, the answer is more complex than expected. Researchers from KU Leuven and collaborating institutions conducted a tightly controlled dietary intervention, known as the "Oatmeal Study", to examine whether restricting food variety could induce convergence in the gut microbiota across individuals. Surprisingly, while participants' diets became nearly identical, their microbiomes did not follow suit. It highlights the importance of individualized responses and underscores the limitations of one-size-fits-all approaches in microbiota-targeted dietary interventions.

The 21-day study followed 18 healthy adults from Flanders, Belgium. It was structured into three phases: a 7-day baseline with habitual diets, a 6-day intervention where participants consumed only oat flakes, whole milk, and still water, and an 8-day follow-up where normal diets resumed. Daily stool samples and weekly blood draws were collected, enabling quantitative microbiome profiling through 16S rRNA gene sequencing paired with flow cytometry. Participants also maintained detailed food diaries, allowing the researchers to link dietary intake with microbial and metabolic outcomes. Notably, microbiome analysis accounted for the estimated 2-day lag between ingestion and egestion, enhancing data accuracy.

Key findings

• Dietary Convergence Achieved

The intervention significantly reduced food intake diversity. Analysis confirmed a sharp drop in dietary variation during the 6-day oat-only phase. Macronutrient intake also declined, with calories reduced by 31.5%, and significant decreases in fat, protein, and carbohydrate consumption. Interestingly, fibre intake increased due to the oat-based diet.

• Microbiome Did Not Converge Across Individuals

One of the study's most surprising findings was the lack of interindividual convergence in gut microbiota. Instead of becoming more similar, microbiome profiles remained distinct and, in some cases, became even more divergent. The effect size (ES) of the dietary intervention on genus-level microbiome variation was 3.4%, but with a striking interindividual range (1.67–16.42%). This undermines the long-held notion that uniform dietary input will yield uniform microbial outcomes and supports the view that host-specific factors such as genetics, baseline microbiota, and metabolic capacity dominate responses to dietary modulation.

• Shift Toward Potentially Dysbiotic Enterotype

A notable shift was observed in microbial community structure. The prevalence of the Bacteroides2 (Bact2) enterotype-often associated with dysbiosis-increased significantly during the intervention, while the more stable Bacteroides1 (Bact1) community declined. These changes were reversed after participants resumed their normal diets. This Bact2 dominance coincided with a marked drop in Faecalibacterium, a butyrate-producing genus known for its anti-inflammatory properties. Given its association with reduced microbial diversity and inflammatory states, the transient rise of Bact2 raises concerns about the health effects of such restrictive diets.

• Microbial Load and Diversity Decreased

Faecal microbial load fell by more than 30% during the intervention, without changes in stool moisture or transit time. This aligns with the reduced caloric intake observed and echoes prior findings showing decreased bacterial biomass under caloric restriction. Furthermore, overall microbiome diversity-as measured by the Shannon index-dropped significantly during the intervention, a pattern that correlates with less mature and resilient microbial ecosystems.

•  Individual Microbiomes Reacted Uniquely

Despite the group-level trends, individuals responded very differently to the same diet. Some showed marked changes in microbial composition, while others remained relatively stable. The authors attempted to identify predictive factors, such as gender or baseline microbiota diversity, but no clear predictors emerged after correction for multiple testing. This unpredictability reinforces the complexity of host–microbiota interactions and suggests that personal traits, rather than just diet, drive microbial changes. Personalized nutrition may be essential to achieving targeted microbiome modulation.

Interpretations and implications

The findings from this study challenge the intuitive belief that simplification of diet should naturally lead to convergence in microbial communities. Instead, they illustrate the resilience of individual microbiota and the importance of pre-existing microbial states in shaping responses to environmental changes. It highlights: (1) Personalized Diets Over Universal Prescriptions: Even under tightly controlled dietary conditions, individuals show unique microbial responses. Future interventions should consider personalized baseline assessments to guide dietary recommendations; (2) Caution in Using Enterotypes as Biomarkers: While Bact2 has been linked with dysbiosis and disease, its transient appearance here in healthy individuals suggests caution when interpreting enterotypes as fixed or pathological markers; (3) Beyond Calories and Macronutrients: The study supports the concept of "successional maturation" of the microbiome, where microbial development is shaped not just by nutrient intake, but also by substrate diversity and transit time. These factors may be equally important as caloric content in shaping gut health.

In conclusion, the "Oatmeal Study" underscores that even radical reductions in dietary diversity do not necessarily bring about uniformity in gut microbiota. Instead, the human microbiome exhibits resilience and individuality, governed by complex host–microbe dynamics. While dietary convergence increased the prevalence of a potentially dysbiotic community type and reduced microbial diversity, the overall effect was modest and highly variable between individuals. These insights are essential for the design of future microbiome-targeted interventions, which must account for individual variability and ecological context.