Longitudinal alterations of gut mycobiota during 2 years after COVID-19 and its correlation with pulmonary sequela.

Pulmonary sequelae associated with COVID-19 are an increasing concern. Emerging evidence suggests that gut dysbiosis may contribute to post-acute COVID-19 syndromes; yet, the specific link between gut mycobiota and pulmonary sequelae remains unclear. We conducted a prospective study with 46 COVID-19 patients and 37 healthy controls. Longitudinal assessments of gut mycobiota were performed at admission, 6 months, 1 year, and 2 years post-discharge using internal transcribed spacer (ITS) 3-4 sequencing. At the 2-year follow-up, pulmonary function tests and chest computed tomography (CT) scans were also performed and correlated with gut mycobiota. While pulmonary function remained well-preserved, radiographic abnormalities persisted in a small subset of patients at 2 years. During the acute phase, fungal richness, as indicated by Chao1 and Shannon indices, was significantly lower than in controls, but gradually returned to normal levels after 6 months of recovery. Genus IMPORTANCE: This article elucidates the intricate process of gut mycobiota reconstitution within a 2-year timeframe following COVID-19 infection and establishes a significant link between the gut mycobiota and the recuperation of pulmonary function. Our research suggests that the gut mycobiota could be utilized as diagnostic indicators for post-acute COVID-19 syndromes and may offer avenues for developing therapeutic interventions.