Chronic fatigue, Lyme, Covid and the gut microbiome

17 Feb, 2022 | Monica Wilde | No Comments

Chronic fatigue, Lyme, Covid and the gut microbiome

Antibiotic use in early life and throughout life “favours an intestinal microbiota composition which might be a risk factor for ME/CFS” (Konig et al., 2022). Clinically, I also find this to be a highly common pattern in patients with stealth infections especially those with lengthy and difficult recoveries. This finding was borne out by the discovery by Morissette et al, 2020 that 80% of post-treatment Lyme patients with ongoing symptoms, including neurocognitive problems, have a distinctive gut microbiome ’signature’. This was independent of whether and how long patients had been on antibiotic therapy.

A poor quality indigenous microbiome leads to gut dysbiosis, altered gut-brain axis activity, increased gut permeability with concomitant bacterial translocation and reduced levels of short-chain-fatty acids, D-lactic acidosis, an abnormal tryptophan metabolism and low activity of the kynurenine pathway. Gut dysbiosis can modify the gut’s fermentation products which affects peripheral mitochondria. Considering the gut-brain axis Konig et al strongly suspect that the microbiome may contribute to neurocognitive impairment.

The gut microbes communicate with the brain by several regulating pathways via the gut–brain axis involved in the physiological activities to maintain homeostasis of the human body. With regard to a link between change in gut microbiome and severely impaired brain function, imbalance of gut microbiota is also associated with Alzheimer’s disease.The gut dysbiosis caused by several factors may aggravate neuroinflammation and other pathologies promoting the development and progression of Alzheimer’s disease (Zhu et al, 2020).

Gut and airway microbiota may also play a role in the pathogenesis of other respiratory viruses such as influenza. Changes in the composition of the intestinal microbiota may negatively impact lung function through systemic immunological effects, and, lung inflammation (in the context of respiratory viral infections) can lead to gut dysbiosis. Brain fog and poor memory are also associated with long Covid-19. During Covid-19 infection, there are significant changes in the composition of the gut and airway microbiota. Liu, Phillipou et al (2021) believe that the gut microbiota may have a more important role than the airway microbiota in Covid-19 infection.

Gut microbiome diversity drops with age which may also be a reason why the elderly have worse outcomes in Covid-19. Gut dysbiosis is also a feature in obesity – another high risk group. It’s a cyclical loop. Not only does poor indigenous microbiome make patients more susceptible to catching a virus, but higher level of proinflammatory cytokines in the blood (due to viral infection) induce dysbiosis of gut bacteria and disruption of the gut barrier (Chattopadhyay & Shankar, 2021). This in turn affects a wide variety of outcomes including cognitive function. 

Ultimately as more and more research emerges, it confirms that a healthy, diverse indigenous microbiome is critical in resisting disease and in the quality of health after either bacterial or viral infection, or chronic fatigue. Humans are now challenged by a global diet that has strayed far from an indigenous diet, the overuse of antibiotics in childhood, and the widespread prevalence of antibiotics in the food chain and environment. These are all factors that will contribute to a rise in neurocognitive conditions, as well as many other, in the decades to come. It underlines the importance of ensuring all patients are meticulous about diets that foster microbiome health. 


Chattopadhyay, I., & Shankar, E. M. (2021). SARS-CoV-2-Indigenous Microbiota Nexus: Does gut microbiota contribute to inflammation and disease severity in COVID-19?. Frontiers in cellular and infection microbiology11, 590874.

König, R. S., Albrich, W. C., Kahlert, C. R., Bahr, L. S., Löber, U., Vernazza, P., Scheibenbogen, C., & Forslund, S. K. (2022). The Gut Microbiome in Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS). Frontiers in immunology12, 628741.

Liu, T., Philippou, E., Kolokotroni, O., Siakallis, G., Rahima, K., & Constantinou, C. (2021). Gut and airway microbiota and their role in COVID-19 infection and pathogenesis: a scoping review. Infection, 1–33. Advance online publication.

Morrissette, M., Pitt, N., González, A., Strandwitz, P., Caboni, M., Rebman, A. W., Knight, R., D’Onofrio, A., Aucott, J. N., Soloski, M. J., & Lewis, K. (2020). A Distinct Microbiome Signature in Posttreatment Lyme Disease Patients. mBio11(5), e02310-20.

Zhu, F., Li, C., Chu, F., Tian, X., & Zhu, J. (2020). Target Dysbiosis of Gut Microbes as a Future Therapeutic Manipulation in Alzheimer’s Disease. Frontiers in aging neuroscience12, 544235.