Long COVID, gut health, and immunity: understanding the connection and how nutrition can help

Research shows that the gut plays a central role in both the persistence of symptoms and recovery in Long Covid. Recent research highlights how chronic inflammation and gut dysbiosis — an imbalance of gut microbes — contribute to Long COVID’s systemic effects.

Fortunately, evidence also suggests that targeted dietary strategies may  help to restore gut balance and strengthen immune resilience.

Illustration taken from Iqbal, 2025

How Long COVID disrupts the gut

During COVID-19 infection, the virus can directly invade intestinal cells via ACE2 receptors, which are abundant in the small intestine. Remnants of the virus may remain in the gut after the initial infection. These remnants are thought to:

• Disrupt amino acid absorption, particularly of tryptophan, needed to make serotonin and maintain gut lining integrity

• Reduce antimicrobial peptide production (our natural defence molecules)

• Weaken the gut barrier, leading to “leaky gut” — where toxins and bacterial fragments escape into the bloodstream, fuelling systemic inflammation

In Long COVID, remnants of the virus and persistent immune activation continue to alter the gut microbiome. Beneficial bacteria such as Faecalibacterium, Bifidobacterium, and Ruminococcus — which produce short-chain fatty acids (SCFAs) like butyrate — tend to decline. At the same time, opportunistic microbes such as Streptococcus and Corynebacterium may overgrow.

Short-chain fatty acids (SCFAs) are small molecules — mainly acetate, propionate, and butyrate — produced when beneficial gut bacteria ferment dietary fibre. They provide energy for intestinal cells, strengthen the gut barrier, reduce inflammation, and help regulate the immune system and metabolism.

This imbalance reduces the production of SCFAs, which are essential for maintaining tight junctions in the intestinal wall, regulating inflammation, and even supporting brain health via the gut-brain axis.

The Gut–Immune–Brain Connection

The gut and immune system are closely linked. In Long COVID:

• Reduced short chain fatty acid levels lead to increased gut permeability and neuroinflammation

• Cytokines and bacterial toxins can cross the gut and blood-brain barriers, activating brain immune cells and disrupting neurotransmitters

• Altered signalling along the vagus nerve and the hypothalamic–pituitary–adrenal (HPA) axis can contribute to fatigue, anxiety, poor sleep, and cognitive “fog”

This means that when the gut barrier is compromised, inflammation becomes systemic — and that may perpetuate Long COVID symptoms.

Nutrition to Restore Gut Integrity in Long COVID

Although research is ongoing, several dietary approaches show promise in restoring microbiome diversity, reducing inflammation, and supporting gut barrier repair.

1. Adopting an anti-Inflammatory Mediterranean-Style diet

A Mediterranean diet—rich in fibre, polyphenols, and omega-3s—has been shown to:

• Lower inflammatory markers such as CRP and IL-17 (Ghosh, 2020)

• Promote SCFA-producing bacteria such as Faecalibacterium prausnitzii and Eubacterium (Liu, 2022; Zhan, 2023)

• Support immune modulation and antioxidant defence

Key components:

• Colourful vegetables and fruits (sources of polyphenols and carotenoids)

• Whole grains, legumes, nuts, and seeds (rich in prebiotic fibres)

• Oily fish and olive oil (sources of omega-3 and monounsaturated fats)

• Limited refined sugars and ultra-processed foods

This Photo by Unknown Author is licensed under CC BY-NC2.

Micronutrient Support for Immunity and Gut Integrity

Certain micronutrients are particularly relevant in Long COVID recovery:

Nutrient	Function	Evidence
Vitamin D	Supports ACE2/Ang1–7/MAS pathway, enhances Bifidobacteria, and reduces inflammation	Low vitamin D levels are independently associated with Long COVID symptoms (Filippo, 2023)
Vitamin C & E	Antioxidants that reduce oxidative stress and inflammation	Shown to lower pro-inflammatory cytokines
Zinc & Selenium	Regulate immune cell signalling and antioxidant enzymes	Deficiency linked to impaired viral clearance
Omega-3 fatty acids (EPA & DHA)	Anti-inflammatory, promote gut microbiome diversity	Found in oily fish, algae, flax, chia

3. Prebiotics, Resistant Starch, and SCFAs

Prebiotics — fibres and resistant starches that feed beneficial bacteria — are central to gut repair.

• Found in legumes, oats, green bananas, onions, garlic, nuts, and seeds.

• Oligosaccharides (like FOS and GOS) are fermented into SCFAs, especially butyrate, the main fuel for colon cells.

• Butyrate supports tight junctions and mucosal barrier repair, reducing permeability and systemic inflammation (Peng, 2009)

Gentle sources of prebiotics for sensitive guts:

• Green banana flour or raw potato starch (low-FODMAP options)

• Cooked and cooled lentils, rice, and potatoes (contain resistant starch)

• Nuts and seeds, these produce high SCFA levels during fermentation

  
  

4. Probiotics for rebalancing the microbiome

Probiotics may help restore the microbial community disturbed by COVID and antibiotic exposure. Evidence from meta-analyses (Neris, 2022; Olaimat, 2020) shows:

• 51% reduction in symptom severity (fatigue, cough, diarrhoea, cognitive issues)

• Improved gut microbiota balance, reducing opportunistic pathogens

• Enhanced immune signalling and antibody production

Helpful strains:

• Lactobacillus plantarum and L. reuteri

• Bifidobacterium longum and B. breve

• Bacillus coagulans and B. subtilis

Food sources

Eating fermented foods on a regular basis is a good way of adding probiotics into your diet. Try using kefir, live yoghurt, sauerkraut, kimchi and kombucha.

5. Protein and Key Amino Acids for Gut Repair

Amino acids are essential building blocks for mucosal healing and immune regulation. It has been shown that absorption of Tryptophan is diminished in Long COVID. Some of the key amino acids needed to support gut health and repair are shown below

Amino Acid	Role	Food Sources
Glutamine	Main fuel for intestinal cells; reduces gut permeability and inflammation (Zhou, 2019)	Soy protein, spirulina, hemp and hard cheese such as parmesan, edam, gouda
Arginine	Enhances immune and GI function	Pumpkin seeds, peanuts, sesame seeds, soy, turkey
Tryptophan	Supports serotonin, melatonin, and gut barrier health (impaired absorption in Long COVID)	Chicken, turkey, pumpkin and chia seeds, tofu, other meat and fish

6. Polyphenols and Antioxidants

Plant compounds such as flavonoids and phenolic acids protect cells and feed beneficial microbes.

• Found in berries, green tea, olive oil, and dark chocolate.

• Reduce oxidative stress and support microbial diversity.

Putting It All Together

Long COVID is not just an immune condition — it’s a gut–immune–metabolic disorder. A multi-targeted nutritional approach that combines:

• Anti-inflammatory whole-food diet

• Essential micronutrients

• Gentle prebiotic and probiotic support

• Adequate protein and amino acids

may help rebuild gut integrity, restore microbial balance, and calm systemic inflammation in Long COVID.

References

• Iqbal NT, Khan H, Khalid A, Mahmood SF, Nasir N, Khanum I, de Siqueira I, Van Voorhis W. Chronic inflammation in post-acute sequelae of COVID-19 modulates gut microbiome: a review of literature on COVID-19 sequelae and gut dysbiosis. Mol Med. 2025 Jan 23;31(1):22. doi: 10.1186/s10020-024-00986-6. PMID: 39849406; PMCID: PMC11756069.

• di Filippo L, Frara S, Nannipieri F, Cotellessa A, Locatelli M, Rovere Querini P, Giustina A. Low Vitamin D Levels Are Associated With Long COVID Syndrome in COVID-19 Survivors. J Clin Endocrinol Metab. 2023 Sep 18;108(10):e1106-e1116. doi: 10.1210/clinem/dgad207. PMID: 37051747; PMCID: PMC10505553.

• Neris Almeida Viana, S., do Reis Santos Pereira, T., de Carvalho Alves, J., Tianeze de Castro, C., Santana C. da Silva, L., Henrique Sousa Pinheiro, L., & Nougalli Roselino, M. (2022). Benefits of probiotic use on COVID-19: A systematic review and meta-analysis. Critical Reviews in Food Science and Nutrition, 64(10), 2986–2998. https://doi.org/10.1080/10408398.2022.2128713Ghosh, T.S. et al. (2020). Gut, 69(7):1218.

• Peng L, Li ZR, Green RS, Holzman IR, Lin J. Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in Caco-2 cell monolayers. J Nutr. 2009 Sep;139(9):1619-25. doi: 10.3945/jn.109.104638. Epub 2009 Jul 22. PMID: 19625695; PMCID: PMC2728689.McLoughlin, R.F. et al. (2017). Am J Clin Nutr, 106(3):930.

• Olaimat, A.N., Aolymat, I., Al-Holy, M. et al. The potential application of probiotics and prebiotics for the prevention and treatment of COVID-19. npj Sci Food 4, 17 (2020). https://doi.org/10.1038/s41538-020-00078-9 

• Zhou, Q.; Verne, M.L.; Fields, J.Z.; Lefante, J.J.; Basra, S.; Salameh, H.; Verne, G.N. Randomised placebo-controlled trial of dietary glutamine supplements for postinfectious irritable bowel syndrome. Gut 2019, 68, 996–1002