How exercise alters gut microbiota in obese people: what a systematic review says

A team of researchers led by Dr. Javier Cansino-Ramirez from the University of Chile conducted the first systematic review of the effects of exercise on the gut microbiota in overweight and obese adults. Their work, published in Applied Physiology, Nutrition and Metabolism, pooled data from 11 clinical studies involving a total of 476 obese participants and 382 healthy volunteers.

Prerequisites

Obesity is associated with disturbances in the gut microbiota, with a decline in beneficial bacteria that produce short-chain fatty acids (SCFA) and a predominance of bacteria that promote inflammation and metabolic imbalance. There has been some evidence that exercise can modulate the microbiome, but it has been limited and of mixed methods.

Methods and selection of studies

• Literature search: MEDLINE, EMBASE, EBSCO, Scopus (as of the end of 2024) according to the PRISMA protocol.
• Inclusion criteria: adults (≥18 years) with a BMI ≥25 kg/m², interventional (controlled and uncontrolled) and cross-sectional studies assessing the association of physical activity levels or exercise programs with microbiota composition (16S rRNA sequencing).
• Risk of bias assessment: RoB 2 for RCT, ROBINS-I for uncontrolled interventions and JBI for cross-sectional studies.

A total of 7 intervention studies (HIIT, aerobics, strength training, 4 to 16 weeks) and 4 cross-sectional studies were included in the review.

Key Results

1. Alpha diversity (within-sample)

   • Interventions have consistently failed to show clear increases in species counts or diversity indices (Shannon, Simpson) following exercise.

   • In cross-sectional studies, more active participants often had slightly higher scores, but the results were inconsistent.

2. Beta diversity (inter-specimen)

   • All intervention protocols showed significant shifts in microbiota composition after training compared to control or baseline (PERMANOVA analysis, p<0.05), indicating the formation of distinct “microbial communities” in active individuals.

3. SCFA producers

   • Exercise of different types resulted in an increase in the relative proportion of the genera Faecalibacterium, Roseburia and Bifidobacterium – key producers of butyrate and propionate, which enhance gut barrier function and reduce systemic inflammation.

4. Functional Predictions

   • Using PICRUSt, the authors showed an increase in genes for butyrate metabolism and a decrease in genes for lipopolysaccharide (LPS) synthesis after moderate- and high-intensity exercise programs.

Limitations and Gaps

• Heterogeneity of protocols: from 4-week HIIT to 16-week mixed programs, different frequency and duration of exercises.
• Small cohorts: Most interventions included 20–30 participants, which reduces statistical power.
• Lack of diet standardization: only three studies controlled for diet, the rest were observational data.
• Lack of RCT for resistance training and neurological analysis of the functional consequences of microbiota shifts.

Practical conclusions

• Personalized approach: When developing exercise programs for weight loss, it is important to take into account the patient's ability to change the microbiota.
• Optimizing exercise: Moderate aerobic and HIIT exercise for 3–5 hours per week produced the most significant shifts in favor of SCFA-producing bacteria.
• Combination with nutrition: Controlling a diet rich in prebiotics (increasing Faecalibacterium and Bifidobacterium ) will enhance the effect of physical activity.

Recommendations for future research

1. Large multicenter RCTs with standardized protocols and mandatory consideration of nutrition.
2. Long-term monitoring of metabolic and clinical outcomes (insulin sensitivity, inflammatory markers).
3. Integrating metagenomics and metabolomics to accurately understand functional changes in the microbiome.

This study highlights that physical activity is not only a stimulus for muscles and the heart, but also a powerful endobiological tool that can improve metabolic and immune health through modulation of gut flora.