Side effects of elemental diets and their effects on the gut microbiome

An elemental diet is typically a liquid, fiber-free diet used in gastrointestinal conditions, among other things. It supplies patients with nutrients, calories, and amino acids while placing no strain on the lower digestive tract. A companion article, Elemental diet explained, covers how it works, its uses, and the research behind it in more depth.

Short-term side effects of an elemental diet include nausea, abdominal pain, diarrhea, and vomiting, particularly when the formula is consumed too quickly. High blood sugar can also occur. [1] Another notable side effect is a shift in gut microbiome composition. [2]

Gastrointestinal side effects

Elemental diets are often poorly tolerated by patients overall. In clinical experience, the taste is a common complaint, and artificial flavoring does not do much to help. Given how unpleasant the taste can be, this alone can be enough to trigger nausea.

Abdominal pain and diarrhea can also result from the altered, fiber-free composition of the diet, which also drives the shifts in the gut microbiome described in the following.

The balance of fat, protein, and carbohydrates in a given formula also appears to affect tolerability. A very low-fat or fat-free elemental diet formula, for example, tends to be more effective and better tolerated in certain conditions. [3]

A note on this content: This article covers a health topic. It is important to have your symptoms evaluated and treated by a qualified healthcare professional. This article cannot replace, and is not intended to replace, care and guidance from a professional.

Other systemic side effects

Allergic side effects

Certain components of an elemental diet formula are not always well tolerated, particularly for people with underlying conditions or allergies. In these cases, allergic symptoms can occur, including a runny nose, sneezing, swelling of the lips or eyelids, itching, and gastrointestinal symptoms. Casein, found in some formulas, for example, can be a problem for people with a cow's milk protein allergy.

Patients with multiple intolerances, mast cell conditions, and/or allergies also frequently have trouble tolerating specific additives, flavoring agents, for example.

Blood sugar fluctuations from elemental diets

To ensure the components of an elemental diet are absorbed in the uppermost part of the intestine, manufacturers use simple carbohydrates that do not require further breakdown, which causes blood sugar to rise quickly. This can lead to blood sugar fluctuations, especially early on, even in people without any underlying issues with glucose metabolism, like diabetes or impaired glucose tolerance.

Blood sugar fluctuations can show up as fatigue, irritability, and sudden intense hunger. A companion article on practical tips for living with an elemental diet covers how to minimize side effects like these.

Changes in the gut microbiome from elemental diets

In chronic inflammatory bowel conditions like Crohn's disease or ulcerative colitis, the gut microbiome is very likely already pathologically altered and produces more toxic byproducts than usual. One theory holds that this drives a loss of immune tolerance toward the body's own gut microbiota, causing the immune system to begin attacking it. [4] [5]

A 2019 study compared the fecal and mucosal gut microbiome of mice after 28 days on an elemental diet against a control group. The mucosal microbiome itself did not change much, but the microbiome found in fecal matter shifted considerably.

Under the elemental diet, for example, Lactobacillus species, generally associated with health benefits, increased compared to a normal diet. Overall microbiome diversity decreased, though, including genera like Akkermansia, Streptococcus, and various others. [6]

Overall, it seems the elemental diet's benefits come largely from how disruptive it is to already pathologically altered gut microbiome, as seen in Crohn's disease, rather than from genuinely improving the microbiome or shifting it toward what's currently considered a "healthy" composition. [7]

Because an elemental diet reduces the pathologically altered gut microbiome seen in chronic inflammatory bowel disease, it also reduces the production of toxic byproducts and lowers overall immune activity. [4] [5]

Intestinal permeability, the "leakiness" of the gut lining, sometimes called "leaky gut," also decreases. [6] This is a genuinely desirable effect, since it means fewer bacterial metabolic byproducts and food components come into contact with the local immune system through a permeable gut lining, reducing the irritation that contact can cause.

Pros and cons at a glance

The gut microbiome after an elemental diet

In small intestinal bacterial overgrowth (SIBO) too, changes to the colonic gut microbiome are a side effect that comes along with reducing the bacterial overgrowth in the small intestine. Antibiotics, the other common SIBO treatment, alter the gut microbiome as well.

After stopping an elemental diet, the gut microbiome typically shifts again, which unfortunately tends to increase relapse risk, particularly in Crohn's disease patients. [8]

Combining elemental and "normal" nutrition

For this reason, modified approaches have been developed for chronic inflammatory bowel disease and severe gastrointestinal allergies, replacing about half of daily caloric intake with an elemental formula. These approaches still show positive long-term effects on disease activity, in Crohn's disease, for example. [9] [10]

This kind of combined approach also tends to be considerably more sustainable long term, without the same toll on quality of life that a diet consisting entirely of elemental formula can bring. [9] Since transitioning to an elemental diet is not easy, a companion article gathers practical, everyday tips for making it more manageable.

Gut microbiome changes after a partial elemental diet

A 2020 study looked at microbiome changes in 12 healthy participants who obtained 900 kilocalories per day from an elemental formula over two weeks, while getting the rest of their calories from their normal diet.

Researchers expected a shift toward a more anti-inflammatory microbiome, but instead found highly variable changes in bacterial genera across the healthy participants over the two-week intervention.

Gut microbiome diversity itself did not decrease in these healthy participants. [11] This contradicts the findings from the animal study mentioned above, where mice were fed an elemental diet for four weeks. [6] It is worth noting, though, that animal models do not necessarily translate directly to humans, and the participants in this human study were still consuming some regular food, and therefore some fiber, throughout the study.

Even two weeks after stopping the partial elemental diet, once participants had returned to their usual diet, measurable changes in the gut microbiome were still detectable, and the original baseline had not been fully restored. [11]

Stopping an elemental diet

Once the intended goal of an elemental diet has been achieved and the underlying condition has settled, the transition back to regular food should be closely coordinated with a healthcare provider.

One option is a gradual transition, where part of daily caloric intake continues to come from the elemental formula for a period of time. This approach has proven successful in conditions like Crohn's disease. [9]

What comes after an elemental diet?

Another study found that reintroducing foods one at a time, and eliminating any that trigger symptoms, can have a positive effect on long-term relapse rates in Crohn's disease patients. [12]

The food intolerances most commonly linked to renewed symptoms after an elemental diet were grains, dairy products, and yeast. [12]

For SIBO, allergies, or mast cell conditions, appropriate dietary strategies and other therapeutic approaches should be used to help prevent bacterial overgrowth or allergic reactions from recurring.

Conclusion: elemental diets based on current scientific understanding

The effect of dietary interventions on the gut microbiome is still not well understood overall, and difficult to predict given individual variation. Considerably more research is needed to fully understand how an elemental diet affects the microbiome, both in the short and longer term.

What is well established is that elemental diets can genuinely help in many serious conditions, and, under ideal circumstances, can be about as effective as low-to-moderate-dose corticosteroids for certain forms of chronic inflammatory bowel disease. [8]

References

[1] Russel RI. Elemental diets. Gut. 1975;16(1):68-79. doi:10.1136/gut.16.1.68

[2] O’Keefe SJ. Tube feeding, the microbiota, and Clostridium difficile infection. World J Gastroenterol. 2010;16(2):139-142. doi:10.3748/wjg.v16.i2.139

[3] Bamba T, Shimoyama T, Sasaki M, et al. Dietary fat attenuates the benefits of an elemental diet in active Crohn’s disease: a randomized, controlled trial. Eur J Gastroenterol Hepatol. 2003;15(2):151-157. doi:10.1097/00042737-200302000-00008

[4] Hunter J. Elemental diet and the nutritional treatment of Crohn’s disease. Gastroenterol Hepatol Bed Bench. 2015;8(1):4-5. Accessed July 23, 2026. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285926/

[5] van der Waaij LA, Kroese FGM, Visser A, et al. Immunoglobulin coating of faecal bacteria in inflammatory bowel disease. Eur J Gastroenterol Hepatol. 2004;16(7):669-674. doi:10.1097/01.meg.0000108346.41221.19

[6] Andoh A, Inoue R, Kawada Y, et al. Elemental diet induces alterations of the gut microbial community in mice. J Clin Biochem Nutr. 2019;65(2):118-124. doi:10.3164/jcbn.19-8

[7] MacLellan A, Connors J, Grant S, Cahill L, Langille MGI, Van Limbergen J. The Impact of Exclusive Enteral Nutrition (EEN) on the Gut Microbiome in Crohn’s Disease: A Review. Nutrients. 2017;9(5). doi:10.3390/nu9050447

[8] Gorard DA, Hunt JB, Payne-James JJ, et al. Initial response and subsequent course of Crohn’s disease treated with elemental diet or prednisolone. Gut. 1993;34(9):1198-1202. doi:10.1136/gut.34.9.1198

[9] Takagi S, Utsunomiya K, Kuriyama S, et al. Effectiveness of an ‘half elemental diet’ as maintenance therapy for Crohn’s disease: a randomized-controlled trial. Alimentary Pharmacology & Therapeutics. 2006;24(9):1333-1340. doi:10.1111/j.1365-2036.2006.03120.x

[10] Hetterich U, Raithel M, Taumann W. Hypoallergene Formulardiäten. Verein zur Förderung der Allergie- und Endoskopieforschung am Menschen e.V. Published February 14, 2015. Accessed July 23, 2026. http://vaem.eu/1395/4-hypoallergene-formulardiaeten/

[11] Miyoshi J, Saito D, Nakamura M, et al. Half-Elemental Diet Shifts the Human Intestinal Bacterial Compositions and Metabolites: A Pilot Study with Healthy Individuals. Gastroenterology Research and Practice. 2020;2020:e7086939. doi:10.1155/2020/7086939

[12] Riordan AM, Hunter JO, Cowan RE, et al. Treatment of active Crohn’s disease by exclusion diet: East Anglian multicentre controlled trial. Lancet. 1993;342(8880):1131-1134. doi:10.1016/0140-6736(93)92121-9