Respiratory Microbiome may have Protective Role Against Long COVID, suggests study

The nasopharynx is the first entry point for respiratory viruses, but the function of the indigenous bacteria during the prolonged stage of COVID-19 infection was not well understood. Therefore, this study attempted to examine the variations in the microbiome structure in patients with different clinical manifestations of COVID-19 and its changes during recovery from infection. To provide a complete evaluation of the phenomenon, the authors selected a varied group consisting of 156 people.

The sample consisted of 25 control subjects, 24 influenza patients, and 107 patients with COVID-19, including 50 with moderate disease and 57 with severe disease. The samples were taken using nasopharyngeal swabs at two crucial stages, namely during the acute infection and 3 months after the infection resolution. The authors used the shotgun metagenomics approach to perform a detailed examination of the microbiome at the species level. Alpha and beta diversity analysis combined with differential abundance analysis allowed us to monitor the changes in the bacterial population.

Key findings:

• From the analysis, it became apparent that the appearance of "protector" species was highly dependent on the clinical treatment in the acute phase.

• Particularly, the consumption of antibiotics was found to be correlated with decreased abundance of "protector" species, thereby potentially enhancing one’s vulnerability to PASC in cases where the body is invaded by another superinfection.

• In a group of 107 patients who suffered from COVID-19 infection, it became evident that the patients with high levels of D. pigrum and Corynebacterium recovered more effectively.

• The longitudinal monitoring for the course of three months proved that although there were many changes within the microbiome, the deficiency of beneficial bacteria was a distinctive feature of PASC syndrome.

The study shows that there is a certain change in the respiratory microbiome that is directly related to the overall recovery process of people infected with COVID-19. It should be noted that the preservation or restoration of balance in the respiratory microbiome can prevent the occurrence of persistent signs of this infection, which in turn means reducing the likelihood of getting PASC. Through understanding which bacteria in the microbiome decrease in numbers in people suffering from Long COVID, researchers have discovered a potential biomarker for risk, along with a new point of intervention.

Reference:

Ward B, Bindels LB, Balligand J, Bearzatto B, Bommer G, Cani PD, De Greef J, Dewulf JP, Gatto L, Haufroid V, Jodogne S, Kabamba B, Pyr dit Ruys S, Vertommen D, Yombi JC, Belkhir L, Elens L. 2026. Association of nasopharyngeal Dolosigranulum pigrum and Corynebacterium species with post-acute sequelae of SARS-CoV-2 in a longitudinal cohort. Microbiol Spectr 14:e02313-25.

https://doi.org/10.1128/spectrum.02313-25