The gut is not simply a passive bystander in long COVID. Research published in Gut in 2022 by Professor Siew Ng and colleagues at the Chinese University of Hong Kong demonstrated that the gut microbiome composition at the time of acute COVID-19 infection predicted who would go on to develop long COVID at six months. Patients with lower microbiome diversity and depleted populations of beneficial Faecalibacterium prausnitzii, Eubacterium rectale, and Bifidobacterium species were significantly more likely to develop persistent symptoms. The gut microbiome appears to be both a determinant of susceptibility and a mediator of ongoing systemic inflammation.
How COVID-19 Disrupts the Gut
SARS-CoV-2 infects cells expressing the ACE2 receptor, and ACE2 is expressed at high density throughout the gastrointestinal tract, particularly in the small intestine. Direct viral damage to enterocytes disrupts the epithelial barrier, allowing bacterial products to translocate into circulation. This bacterial translocation is a potent driver of the systemic immune activation that characterises long COVID. A study published in the Lancet Microbe in 2021 found evidence of gut dysbiosis and bacterial translocation in hospitalised COVID-19 patients that persisted well beyond discharge.
Viral RNA has been detected in stool samples from long COVID patients at six months and beyond, even when nasopharyngeal swabs are negative, suggesting that the gut acts as a viral reservoir that continues to drive immune activation. The disrupted microbiome that follows acute infection may impair the immune system's capacity to clear this viral persistence.
The Case for Dietary Fibre
Dietary fibre is the primary substrate for gut bacterial fermentation. When beneficial bacteria such as Faecalibacterium prausnitzii and Bifidobacterium species ferment soluble fibre, they produce short-chain fatty acids including butyrate, propionate, and acetate. Butyrate is the primary energy source for colonocytes, maintains gut barrier integrity, and actively suppresses inflammatory signalling in immune cells. A diet high in diverse plant fibre is the most evidence-based strategy for restoring these depleted bacterial populations.
Research from the Sonnenburg laboratory at Stanford, published in Cell in 2021, conducted a randomised controlled trial comparing a high-fibre diet to a high-fermented-food diet and found that the high-fibre diet significantly increased microbial diversity and reduced a panel of inflammatory proteins, including several that are elevated in long COVID. The effect was dose-dependent and apparent within ten weeks.
Best Plant Foods for Gut Restoration in Long COVID
- Legumes: lentils, chickpeas, kidney beans, and black beans are among the richest sources of prebiotic fibre, including resistant starch and fructooligosaccharides, and are the food group most consistently associated with microbiome diversity across population studies
- Jerusalem artichoke and chicory root: the richest dietary sources of inulin, a prebiotic fibre that selectively feeds Bifidobacterium; start with small amounts as they can cause gas during the adaptation period
- Garlic and onions: contain fructooligosaccharides and have prebiotic effects well-supported by in vitro and human studies
- Oats: beta-glucan from oats has prebiotic effects and additionally moderates post-meal blood glucose responses, which tend to be dysregulated in long COVID
- Diverse vegetables: aim for 30 or more different plant foods per week; the landmark American Gut Project found that people eating more than 30 plant varieties per week had significantly higher microbiome diversity than those eating fewer than 10
- Fermented plant foods: kimchi, sauerkraut, tempeh, and miso provide live bacterial cultures that contribute to microbial diversity in the short term while the fibre-based restoration proceeds
The Gut-Brain Axis and Long COVID Cognitive Symptoms
Cognitive impairment, colloquially referred to as brain fog, is one of the most disabling long COVID symptoms and may be partly mediated through the gut-brain axis. The vagus nerve carries signals between gut and brain bidirectionally, and a disrupted gut microbiome alters vagal signalling. Additionally, lipopolysaccharides from gram-negative bacteria that translocate through a leaky gut barrier trigger neuroinflammation via microglial activation. Restoring gut barrier integrity through dietary fibre, zinc, vitamin D, and omega-3 fats may therefore have direct cognitive benefits.
A Practical Approach
Those with significant gut symptoms in long COVID should introduce high-fibre plant foods gradually, as a rapid increase in fibre can exacerbate bloating and discomfort if the bacterial populations that ferment fibre are depleted. Starting with cooked vegetables and lentils before introducing raw foods and high-inulin sources is a sensible progression. Keeping a food and symptom diary during this period helps identify specific foods that worsen symptoms, which varies between individuals.
Sources
- Lui, G.C.Y., et al. (2022). Gut microbiota in long COVID patients and matched COVID-recovered patients. Gut, 71(6), 1152-1164.
- Zuo, T., et al. (2021). Gut microbiota of COVID-19 recovered patients returns to uninfected status in a minority-directed manner. Gastroenterology, 160(7), 2422-2432.
- Wastyk, H.C., et al. (2021). Gut-microbiota-targeted diets modulate human immune status. Cell, 184(16), 4137-4153.
- Sonnenburg, J.L., & Sonnenburg, E.D. (2022). Vulnerability of the industrialised microbiota. Science, 378, 6619.
- Vujkovic-Cvijin, I., et al. (2020). Dysbiosis signatures of gut microbiota in COVID-19 patients. Cell Host and Microbe, 28(2), 289-301.