The gut microbiome—our inner ecosystem of trillions of microorganisms—plays a central role in digestion, immunity, metabolic health, and even mood. One of the most powerful levers we have to influence this microbial community is diet.

1. Plant-Rich Diets (Vegetarian & Vegan)

Vegetarian and vegan diets, abundant in fibre, polyphenols, and prebiotics, consistently show a positive impact on gut health:

• Increased diversity: Fibre-rich diets support the growth of Bifidobacteria and Lactobacillus, considered beneficial microbes.

• Higher SCFA production: Complex carbohydrates are fermented into short-chain fatty acids (SCFAs) like butyrate, which regulate inflammation, enhance gut barrier integrity, and improve insulin sensitivity via GLP-1 secretion.

• Immune modulation: Plant-based eaters often show reduced pro-inflammatory bacterial species compared to omnivores.

2. Mediterranean Diet

The Mediterranean diet—rich in vegetables, fruits, whole grains, legumes, olive oil, and fish—has the strongest evidence for supporting microbial balance:

• Boosts butyrate producers: Promotes Faecalibacterium prausnitzii and Roseburia, both associated with anti-inflammatory effects.

• Reduces pathogenic species: Linked to decreased levels of Proteobacteria and endotoxin-producing bacteria.

• Metabolic benefits: Associated with lower risk of obesity, cardiovascular disease, and type 2 diabetes, partially mediated by the microbiome.

3. Western Diet

The Western diet, high in refined sugars, processed foods, and saturated fats, is consistently detrimental to microbial health:

• Reduced diversity: Leads to dysbiosis, a disrupted microbiome linked with obesity, insulin resistance, and inflammatory bowel disease.

• Loss of beneficial species: Fibre deficiency decreases SCFA producers.

• Overgrowth of pro-inflammatory bacteria: Promotes Enterobacteriaceae and other endotoxin producers.

  
  

4. Ketogenic Diet

The ketogenic diet (KD), very low in carbohydrates and high in fats, shows more complex effects:

• Reduced fibre-fermenters: Lower Bifidobacteria and Roseburia due to limited carbohydrate intake.

• Microbiota reshaping: Increases Akkermansia and alters the Bacteroidetes:Firmicutes ratio, potentially aiding weight loss and neurological disorders.

• Reduced Th17 inflammation: KD-associated microbes can lower intestinal Th17 cells, with benefits for epilepsy and autoimmune conditions.

5. Carnivore Diet

The carnivore diet, consisting solely of animal products, has very limited research:

• Case study evidence: A single published study found dominance of Firmicutes and fiber-degraders like Faecalibacterium despite the absence of plant foods.

• No major diversity loss (short-term): Suggesting microbial resilience, though long-term effects on SCFAs, inflammation, and metabolic risk remain unknown.

6. Omnivorous Mixed Diets

Omnivores consuming a balance of plant and animal foods show intermediate microbiome profiles:

• Diversity depends strongly on fibre intake rather than animal protein.

• Moderate meat consumption combined with high plant fibre may provide both microbial stability and functional diversity.

Comparative Summary

Mechanisms of Influence

1. Fiber and SCFAs

   
   

   • Diets rich in plants increase butyrate and other SCFAs, improving gut barrier integrity, reducing inflammation, and enhancing insulin sensitivity through GLP-1 stimulation.

   
   

2. Fat and Protein

   
   

   • High-fat, low-fibre diets (ketogenic, carnivore) shift microbiota toward protein and fat metabolisers, which may benefit ketosis but limit SCFA availability.

   
   

3. Immune Modulation

   
   

   • Plant-rich and Mediterranean diets increase anti-inflammatory microbes, while ketogenic diets may suppress specific inflammatory immune pathways.

   
   

(Yersin and Vonaesch, 2024) 

Conclusion

Diet is the most powerful determinant of gut microbiome composition and function.

• Plant-rich and Mediterranean diets are strongly associated with higher diversity, increased SCFA production, and anti-inflammatory profiles.

• Western diets disrupt microbial balance and contribute to metabolic disease.

• Ketogenic diets reshape the microbiome in ways that may offer therapeutic benefits but reduce SCFA producers.

• Carnivore diets remain poorly studied, with early evidence suggesting stability but unclear long-term outcomes.

Ultimately, a diverse, fibre-rich diet remains the most evidence-based approach to sustaining a healthy gut microbiome, though specific therapeutic diets may have targeted benefits.

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References

• David, L.A. et al. (2014) ‘Diet rapidly alters the human gut microbiome’, Nature, 505(7484), pp. 559–563. https://doi.org/10.1038/nature12820.

• Garcia-Mantrana et al. (2018) ‘Shifts on Gut Microbiota Associated to Mediterranean Diet Adherence and Specific Dietary Intakes on General Adult Population’, Frontiers in Microbiology, 9, p. 890. https://doi.org/10.3389/fmicb.2018.00890.

• Haller, D. (2018) The Gut Microbiome in Health and Disease. Cham: Springer International Publishing. https://doi.org/10.1007/978-3-319-90545-7.

• Karačić, A. et al. (2024) ‘The gut microbiome without any plant food? A case study on the gut microbiome of a healthy carnivore’, Microbiota and Host, 1(2), p. 100006. https://doi.org/10.1530/MAH-24-0006.

• Olson, C.A. et al. (2018) ‘The gut microbiota mediates the anti-seizure effects of the ketogenic diet’, Cell, 173(7), pp. 1728–1741.e13. https://doi.org/10.1016/j.cell.2018.04.027.

• Paoli, A. et al. (2013) ‘Therapeutic uses of very-low-carbohydrate (ketogenic) diets: a review’, European Journal of Clinical Nutrition, 67(8), pp. 789–796. https://doi.org/10.1038/ejcn.2013.116.

• Tomova, A. et al. (2019) ‘The Effects of Vegetarian and Vegan Diets on Gut Microbiota’, Frontiers in Nutrition, 6, p. 47. https://doi.org/10.3389/fnut.2019.00047.

• Wu, V. C. H. (ed.) (2022) The Gut Microbiome: Bench to Table. Boca Raton: CRC Press. https://doi.org/10.1201/b22970

• Yersin, S. and Vonaesch, P. (2024) ‘Small intestinal microbiota: from taxonomic composition to metabolism’, Trends in Microbiology [Preprint]. https://doi.org/10.1016/j.tim.2024.02.013.

• Zinöcker, M.K. and Lindseth, I.A. (2018) ‘The Western Diet–Microbiome-Host Interaction and Its Role in Metabolic Disease’, Nutrients, 10(3), p. 365. https://doi.org/10.3390/nu10030365.