A study led by researchers at the University of Dundee has reported marked differences in the oral microbiome of people with long COVID. The team analysed saliva samples from 771 patients who had previously been hospitalised with COVID-19, grouping participants by the severity of their ongoing symptoms. Those classified as having extreme long COVID showed clear microbial differences in the mouth and airways compared with people who did not have the condition.
The researchers found that the microbiome changes in people with long COVID were associated with a range of systemic symptoms. These included:
One specific microbial pattern the team reported was an over-abundance of bacteria that produce lactic acid. This increase was linked to signs of inflammation detected in patients’ blood samples.
The study authors emphasised that their work could not resolve whether the altered microbiome was a consequence of the COVID-19 infection or if it pre-dated infection and therefore contributed to a person’s risk of developing long COVID. The article notes earlier research from 2023 showing that COVID-19 can reduce oral microbiome diversity, but the present analysis does not establish cause and effect.
Lead author Dr Daniela Alferes de Lima Headley commented on the findings and the broader problem: “We know that millions of people worldwide are still affected by long COVID and its cause is still unknown. Long COVID affects multiple organs. The microbiome is important to maintain health throughout the body, so it is a strong candidate for something that may contribute to long COVID.”
Professor James Chalmers, chair of respiratory research at the University of Dundee, highlighted the clinical importance of understanding causes. He said the field urgently needs to know what causes long COVID because it remains a major healthcare problem. He pointed out that the microbiome can be altered by interventions such as antibiotics and probiotics, and expressed hope that these results will stimulate further research and, ultimately, treatment trials for people living with long COVID.
This research is part of PHOSP-COVID, a consortium of UK researchers working to understand and improve long-term health outcomes for people hospitalised with COVID-19. The PHOSP-COVID programme has produced multiple studies aimed at characterising persistent problems after acute infection.
The article also references prior research from 2023 that demonstrated COVID-19 infection can reduce the diversity of the oral microbiome. However, the present study’s findings add new detail by linking specific microbial changes to particular long COVID symptom clusters, while leaving open the question of temporal direction and causality.
Professor Raquel Duarte, head of the European Respiratory Society’s assembly on infectious diseases, framed the findings in the wider social and clinical impact of long COVID. She noted that millions continue to live with disabling consequences, including persistent respiratory and cognitive symptoms that affect the ability to work, study or manage daily activities, with wider implications for families and health services.
Because the study did not establish whether microbiome changes are a cause or an effect of long COVID, the immediate implication is a need for further investigation. The authors and commentators suggest several avenues:
Professor Chalmers specifically noted the potential for treatment trials in the future, stating the hope that the findings will stimulate more research and, eventually, clinical trials to help people with the condition.
The source article makes clear the limits of the published analysis. It does not report details on whether the microbiome differences observed were present prior to infection, nor does it provide the study’s full methodological details, such as exact sequencing methods, control groups beyond the patient stratification, or the timing of sample collection relative to acute illness. The article also does not report effect sizes, statistical analyses or other quantitative measures beyond the descriptive associations and the sample size of 771 patients.
The researchers and commentators call for more work to answer remaining questions about long COVID and the microbiome. Key next steps suggested in the article include:
Until such studies are completed, the findings add to a growing body of evidence linking post-COVID ill health with changes in microbial communities but stop short of identifying a proven treatment pathway.
The study adds a new observation to the clinical picture of long COVID: people with severe ongoing symptoms after hospitalisation showed distinct differences in the oral microbiome, including an over-representation of lactic acid–producing bacteria associated with blood markers of inflammation. The work forms part of broader research efforts under PHOSP-COVID to define long-term outcomes after COVID-19 and suggests that the microbiome is a plausible target for further investigation. However, based on the information reported in the article, there is no direct evidence yet that microbiome-targeted treatments will improve long COVID symptoms; the article calls for further research and clinical trials to explore that possibility.
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