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Long Covid microbiome research backs up my clinic work

Exciting new research helps confirm gut microbiome changes are associated with Long Covid. Published in the British Medical Journal’s GUT, it also backs up my findings in my Microbiome Analysis practice working with people who have Long Covid over the past 18 months, and my original rationale for their treatment.

Images: Figures from the paper (mapping symptoms to bacterial changes), and a screenshot of the article

Several clinical studies have already supported the theory that a healthy gut microbiome may help protect us from the most severe symptoms of acute COVID, but few studies have looked at the role of the microbiome in Long Covid (or as this study calls it Post-Acute Covid Syndrome, PACS).

Study design

In this study, researchers tracked changes in the gut microbiome of 106 patients with varying degrees of COVID severity, at 3 different hospitals between February and August 2020, and in a comparison group of 68 people who didn't have COVID, over the same period. They checked for the presence of the 30 most commonly reported Long Covid symptoms at 3 and 6 months after infection. They also used a 6-minute distance walk test to measure aerobic capacity and endurance.

Key findings

Microbiome stool tests revealed that key beneficial bacteria are depleted in those with Long Covid, especially Bifidobacteria, Faecalibacterium and Blautia obeum. I have definitely found this to be extremely common in the stool tests I’ve analysed since I first began supporting people with Long Covid back in September 2020. Significantly, all these species play a critical role in reducing inflammation, bearing out my original aim of increasing the anti-inflammatory capacity of the microbiome. This is important because inflammation does seem to be the basis of many of the Long Covid symptoms, including inflammation of blood vessels and micro-clotting.

The tests also showed that inflammation-causing bacteria are increased in those who have Long Covid, including Ruminococcus gnavus (a species that degrades the mucus lining our gut) and Bacteroides vulgatus. I have also found these are increased in most of the stool samples I have analysed, together with several other inflammatory bacteria.

From these changes, the researchers concluded an individual’s gut microbiome profile may affect their susceptibility to Long Covid. They also mapped different bacterial species to different symptoms (with some pretty diagrams)! This is really interesting and useful research, but we really need a bigger sample size for that to be conclusive.

The researchers compared microbiomes of each individual at hospital admission to see whether there was any difference for those who had symptoms at 6 months. The patterns they saw suggest that the composition of someone’s microbiome at the time they catch COVID could predict whether they get longterm symptoms,

The researchers suggested microbiome profiling could therefore be used to determine someone’s risk of Long Covid. They also found that those who didn't develop Long Covid had fewer changes in bacterial species at hospital admission, and this had recovered completely after 6 months.

Future considerations

All in all, a very exciting and important study. I hope this will not only lead to better treatment options, including microbiome interventions, for people who have Long Covid, but also those with other fatigue conditions. Certain conditions, such as IBS and previous post-viral fatigue, have been shown to dramatically increase someone's risk for Long Covid, so this study suggests microbiome repair may also empower people to change their Long Covid risk profile.

I hope this kind of clinical evidence will also help lift the stigma of post-viral fatigue conditions and reduce the medical gaslighting (dismissal of symptoms) that prevents proper medical attention and support.


Liu Q, Mak JWY, Su Q, et al Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome, Gut, 26 January 2022.

Images: screenshots showing the main points, and a chart showing microbiome changes.

Viola Sampson BSc is a Microbiome Analyst practising in London UK and online. You can book a consultation, or get in touch to find out more.

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