Oral and Lung Microbiome Changes Linked to Severe Long Covid Symptoms

Because COVID-19 initially affects the respiratory tract, the airway microbiome may offer clues beyond previously observed gut microbiome changes. New findings now show distinct oral and lung microbiome patterns in people with the most severe long Covid symptoms.

The University of Dundee led the PHOSP-COVID research, which examined microbiome differences in people previously hospitalized with COVID-19. The study used DNA sequencing-based microbiome analysis of saliva and sputum samples to identify microbes present in the mouth and lungs. PHOSP-COVID is continuing to investigate the burden and management of long Covid.

The research included 771 people treated for COVID-19 between February 2020 and March 2021 at one of 38 UK hospitals. Participants were divided into four groups based on symptom severity five months after hospital discharge: very severe, severe, moderate, and mild. Six months after discharge, researchers collected saliva samples from the mouth and sputum samples from the lungs, then compared microbial variety and quantity with patient symptoms.

People with very severe long Covid showed clear differences in the microbiome of both the mouth and lungs compared with those without severe long Covid. The differences were linked to reduced lung function, neurocognitive symptoms including brain fog and problems with memory, attention, and concentration, and gastrointestinal symptoms including pain, nausea, diarrhea, and loss of appetite. An overabundance of lactic acid-producing bacteria was also associated with long Covid symptoms and with signs of inflammation in blood samples.

The findings were published in the European Respiratory Journal on October 11, 2026. The researchers noted that it remains unclear whether the microbiome changes existed before COVID-19 infection or developed afterward. They also stated that further work is needed to understand whether these microbiome changes improve over time and whether they could inform future treatment studies.

“What we don’t know is whether these changes came before a Covid infection, or whether the changes happened following a Covid infection. We also do not know what will happen to the microbiome in patients in subsequent years. We would love to know whether these changes get better with time,” said Professor James Chalmers, Chair of Respiratory Research at the University of Dundee.

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