CIDRAP-Long-COVID symptoms may be linked to bacterial mix in the mouth, lungs

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Long-COVID symptoms may be linked to bacterial mix in the mouth, lungs

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Long-COVID symptoms may be linked to bacterial mix in the mouth, lungs​

Mary Van Beusekom, MS

October 12, 2026
COVID-19


People who have severe long COVID have a very different oral and pulmonary microbiome than those with mild symptoms, and the differences are linked to specific symptoms, which scientists say may lead to a clearer picture of the condition and better ways to treat it.

The findings come from an observational study by the longitudinal, multicenter UK Post-hospitalisation COVID-19 (PHOSP-COVID) Collaborative Group and published yesterday in the European Respiratory Journal.

The researchers recruited 771 adults, grouping them by severity of ongoing health problems and symptom subgroups. Six months after hospital release, the team took saliva samples from the patients’ mouths and sputum samples from their lungs for sequencing and bacterial-diversity analysis, and participants completed symptom questionnaires.

The study participants had been released from one of 83 UK hospitals after COVID-related admission from February 2020 to March 2021. The average participant age was 57.5 years, and 38.5% were women.

“Acute COVID-19 is a pulmonary disease with the infection phase known to alter the oral and airway microbiota, with shifts in microbial composition linked to disease severity and immune responses,” the authors wrote. “These microbial communities are not isolated; they interact with other organ systems through communication pathways such as the gut-lung and the oral-brain axes, which have been associated with other chronic diseases.”

Possible role for lactic acid–making bacteria ​

In the group with very severe long-COVID symptoms, the oral microbiota was significantly less diverse than that in the group with mild symptoms at six months post-hospitalization. This group had the highest frequency of breathlessness, fatigue, impaired lung function, and reduced exercise capacity.
We also found that changes in the airway microbiome were linked not just to lung problems, but also to symptoms like brain fog and gut symptoms, suggesting the lung microbiome could have effects on health more broadly.
James Chalmers, MD, PhD
Impaired lung function and neurocognitive symptoms were linked to separate distinct oral microbiota profiles, whereas gastrointestinal (GI) symptoms were associated with a distinct sputum microbiota profile.

In participants with ongoing symptoms, there was an overabundance of lactic acid bacteria, which was tied to inflammation and poorer health outcomes. This shift suggests a possible role for lactic acid–producing bacteria and host immune response in more severe long COVID, the authors said.

The sputum microbiota analysis produced similar findings at six months, but bacterial composition didn’t differ appreciably by symptom severity.

“People who had the worst symptoms five to six months after Covid infection had big changes in the microbiome in their mouth and lungs,” senior author James Chalmers, MD, PhD, of the University of Dundee, said in a news release from the European Respiratory Society, which publishes the journal.

“We also found that changes in the airway microbiome were linked not just to lung problems, but also to symptoms like brain fog and gut symptoms, suggesting the lung microbiome could have effects on health more broadly.”

Which came first?​

But the authors cautioned that it’s not clear whether the changes in microbiota occurred before or after COVID-19 infection or whether the microbiome recovers over time. “Understanding what causes it could lead to better treatments; the microbiome can be changed using antibiotics, probiotics, or other measures,” Chalmers said.

Raquel Duarte, MD, head of the European Respiratory Society’s assembly on infectious diseases based at the University of Porto in Portugal, said in the release that long COVID can have devastating consequences for patients, their families, health services, and society.

“Six years after the start of the pandemic, we still do not fully understand why some people develop long Covid or how best to support their recovery,” said Duarte, who was not involved in the trial. “If these associations are confirmed, they may ultimately help us identify new ways to predict, prevent or treat the most disabling forms of long Covid.”