How Keto and Low-Carb Diets Could Be Harming Your Gut Health

Low-carbohydrate diets have gained a lot of popularity over recent years, with much evidence showing their effectiveness in weight loss and improved cardiovascular health (1,2).  However, an often-neglected issue with Low carb diets is the effect they could be having on the health and diversity of our gut and our microbiome (3,4,5,6,7,8).

Two popular low carb diets are the Atkins diet and the Ketogenic diet.  The traditional Atkins diet recommends a very low intake of carbohydrates and a relatively high consumption of foods high in protein (9), essentially making it a low-carb, high-protein diet. The Ketogenic or keto diet which shares many similarities with the Atkins diet, promotes a drastic reduction in the consumption of carbohydrates and replacing these with fat (10). 

A generic low-carb diet is also very popular today, where less emphasis is placed on how you replace carbohydrates, as long you as you keep their consumption at a minimum.

How low-carb diets may be affecting our gut health

Low-carb diets discourage the consumption of high-carb fruits (bananas, apples, oranges etc), high-carb vegetables (carrots, turnips etc), starches (potatoes, sweet potatoes etc), legumes (lentils, beans, chickpeas etc) and grains (wheat, spelt, rye, barley, rice etc) (9,10).  If these foods are not adequately replaced with low-carb, high-fibre foods (such as kale, spinach, broccoli, asparagus etc), the amount of fermentable carbohydrates exposed to our gut microbiota will be significantly reduced.

The effect of reduced gut exposure to fermentable carbohydrates

The reduction of fermentable carbohydrate exposure in our gut results in the reduced production of carbohydrate-related metabolites (breakdown products of carbohydrates) (3). Butyrate, one of these important metabolites, has been shown to reduce both gut inflammation and the risk of colorectal cancer (4,5).  Additionally, current evidence suggests that LC diets result in gut dysbiosis, and more specifically in a significant reduction of butyrate-producing bacteria (Roseburia species, Bilfobacterium species and the E.rectale group).

Despite there being no published research on the long-term gastrointestinal effects of decreased butyrate production in our gut, it is plausible to suggest that LC diets may increase the risk of chronic gastrointestinal disorders and colorectal cancer (3).  

The promotion of increased red meat consumption

LC diets traditionally promote a high consumption of red meat – as a means of ensuring high protein and high fat intake – which creates a number of gut health issues.  The intake of red meat is potentially associated with colorectal cancer (4,5), and as a result the World Health Organization has labelled red meat consumption as a Group 2A carcinogen (12). Eating high amounts of red meat also increases saturated fat intake, which has been linked with gut dysbiosis (11) and gut inflammation (7).  

An eco-Atkins diet has been developed that encourages the substitution of red meat with high protein plant foods (13); an important adaptation that mitigates these risks.

Our Recommendation

While there is evidence supporting the benefits of Low carb diets with regards to weight loss and reducing cardiovascular disease risk (1,2), we recommend carefully considering how they could negatively affect gut health.  

Further research is required to validate the plausibility of an increased risk of long-term gastrointestinal disorder and colorectal cancer development as a result of long-term adherence to Low carb diets.

Key Points

  • Low-carb diets discourage the consumption of many high fibre foods which, if not adequately replaced, reduces gut exposure to fermentable carbohydrates.
  • Reduced gut exposure to fermentable carbohydrates results in a decrease in important metabolite production in the gut.  A reduction in one of these metabolites, butyrate, has been linked with an increased risk of gut inflammation and colorectal cancer.
  • Reduced gut exposure of carbohydrates has also been linked with specific alterations in gut microbiota, further decreasing the production of important metabolites.
  • Low-carb diets traditionally promote high red meat consumption, which has been linked with colorectal cancer, gut inflammation and gut dysbiosis. The eco-Atkins diet is an alternative that mitigates these risks.


  1. Hession, M., Rolland, C., Kulkarni, U., Wise, A., & Broom, J. (2009). Systematic review of randomized controlled trials of low‐carbohydrate vs. low‐fat/low‐calorie diets in the management of obesity and its comorbidities. Obesity reviews10(1), 36-50. Available from:
  2. Yang, M. U., & Van Itallie, T. B. (1976). Composition of weight lost during short-term weight reduction. Metabolic responses of obese subjects to starvation and low-calorie ketogenic and nonketogenic diets. The Journal of clinical investigation58(3), 722-730. Available from:  
  3. Brinkworth, G. D., Noakes, M., Clifton, P. M., & Bird, A. R. (2009). Comparative effects of very low-carbohydrate, high-fat and high-carbohydrate, low-fat weight-loss diets on bowel habit and faecal short-chain fatty acids and bacterial populations. British journal of nutrition101(10), 1493-1502. Available from:
  4. Johnstone, A. M. (2012). Safety and efficacy of high-protein diets for weight loss. Proceedings of the Nutrition Society71(2), 339-349.  Available from:
  5. Louis, P., Hold, G. L., & Flint, H. J. (2014). The gut microbiota, bacterial metabolites and colorectal cancer. Nature Reviews Microbiology12(10), 661. Available from:
  6. De Wit, N., Derrien, M., Bosch-Vermeulen, H., Oosterink, E., Keshtkar, S., Duval, C., … & van der Meer, R. (2012). Saturated fat stimulates obesity and hepatic steatosis and affects gut microbiota composition by an enhanced overflow of dietary fat to the distal intestine. American Journal of Physiology-Gastrointestinal and Liver Physiology303(5), G589-G599.  Available from:
  7. Kennedy, A., Martinez, K., Chuang, C. C., LaPoint, K., & McIntosh, M. (2008). Saturated fatty acid-mediated inflammation and insulin resistance in adipose tissue: mechanisms of action and implications. The Journal of nutrition139(1), 1-4. Available from:
  8. Duncan, S. H., Belenguer, A., Holtrop, G., Johnstone, A. M., Flint, H. J., & Lobley, G. E. (2007). Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Applied and environmental microbiology73(4), 1073-1078. Available from:
  9. Healthline. The Atkins Diet: Everything You Need to Know (Literally). Available from:
  10. Healthline. The Ketogenic Diet 101: A Detailed Beginner’s Guide. Available from:
  11. De Wit, N., Derrien, M., Bosch-Vermeulen, H., Oosterink, E., Keshtkar, S., Duval, C., … & van der Meer, R. (2012). Saturated fat stimulates obesity and hepatic steatosis and affects gut microbiota composition by an enhanced overflow of dietary fat to the distal intestine. American Journal of Physiology-Gastrointestinal and Liver Physiology303(5), G589-G599.  Available from:
  12. WHO: Q&A on the carcinogenicity of the consumption of red meat and processed meat. Available from:
  13. Katz, D. L., & Meller, S. (2014). Can we say what diet is best for health?. Annual review of public health35, 83-103. Available from:

Stewart Dunlop

Content Manager at The Good Gut
Stewart is the content and marketing manager at The Good Gut - a new project devoted to maintaining gut health. Being a passionate writer, he aims to raise the awareness of the importance of gut health to the overall well-being of any individual.

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