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The Gut Microbiome and Long Covid: A clinical practice case study

Updated: Nov 1, 2023

My research has been focused on the connection between the different microbiomes and SARS-CoV-2/Long Haul Covid for the past 2 years. A recent study has just been released stating that SARS-CoV-2 likely infects the gastrointestinal tract (1), which has led to a shift in healthcare towards using gut microbiome manipulation to treat Long-Term Illness.

There is some really interesting and exciting studies coming to light that favourably support the need to turn our attention to microbiome manipulation, but how we can transfer this knowledge into clinical practice. to support the recovery from Long Covid? Here I present a case study that focuses on the gut microbiome and Long Covid recovery.



Male, 14 years old, unvaccinated, PCR Covid Positive July 2021. Symptoms experienced were fatigue, high temperature, loss of taste and smell and a chesty cough. The worse of the symptoms cleared after 10 days, but the fatigue remained along with a slightly annoying cough. The fatigue was still present at our consultation back in November 2021. Of note was a previous food poisoning event with Clostridium perfringens in June 2021 and was given a 5 day course of penicillin.

Lab Tests

Blood tests all normal (Including vitamin D status)

GI Effect comprehensive stool analysis showed marked dysbiosis - and a reduction of Lactobacillus species, Bifidobacterium spp. alongside other major butyrate producing commensals, including Faecalibacterium prausnitzii and Roseburia hominis that may contribute to intestinal hyper-permeability.

Possible connection between SARS-CoV-2 and the protection provided by the gut microbiome - particularly butyrate producers (2)


  • A food plan to increase fibre, polyphenols, colour and diversity, to encourage the growth of commensal species

  • An adjusted "teenage boy" version of my gut healing and oral hygiene protocols

  • Negotiated an adjustment to the the diet to reduce reliance on high sugar foods just while we supported the gut

  • Added specific fermented foods and a targeted probiotic.

Outcome 1 month later

Energy levels have normalised, he has resumed exercise and after school activities and can stay up later in the evening. Concentration levels have greatly improved and gut function is normal.

This boy continues to do well in all of these areas even to this day.

What I learned from this particular case

This case was relatively straight forward. Due to his young age, once the underlying metabolic dysfunction was addressed symptoms disappeared and the body was able to function normally.

The gut microbiome would have been negatively impacted by the bout of food poisoning and subsequent antibiotics; this may have made this boy more susceptible to contracting the virus.

For me this case further solidified my hypothesis at the start of the pandemic that the gut microbiome is one of the important target areas for the resistance, resilience and recovery from Covid-19 and Long Covid. However clinicians must not become complacent and must not forget to address all other areas of a persons health. Simply focusing on the gut microbiome alone is not enough for more severe or complex cases.



(1) Natarajan, A., Zlitni, S., et al., 2022. Gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA suggest prolonged gastrointestinal infection. Med.

(2) Kim, H.S., 2021. Do an altered gut microbiota and an associated leaky gut affect COVID-19 severity? mBio, [online] 12(1), pp.1–9. A


Work with me

Rachel Jessey holds a Masters Degree in Personalised Nutrition a Diploma in Naturopathic Nutritional Therapy and is a registered Naturopath and scientific researcher. She has undertaken extra training in function medicine and has a keen interest in the immune system and autoimmune conditions. As well as conducting ongoing research Rachel runs a busy eConsult clinic in the UK and has been in clinical practice for over 12 years.

For more on improving Resistance, Resilience and Recovery take a browse though my website and check out my free downloads and consultation options. I am due to launch my 3R nutrition programme that focuses on nutrition to support your immune resilience. Please hit the button below to go on to my waiting list and I will send you the details

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