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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\u20134 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\n                      <jats:italic toggle=\"yes\">Candida<\/jats:italic>\n                      , elevated during the acute phase, reverted to control levels after 6 months. At the 2-year follow-up, there was an increased presence of\n                      <jats:italic toggle=\"yes\">Hanseniaspora<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Issatchenkia<\/jats:italic>\n                      , and\n                      <jats:italic toggle=\"yes\">Saturnispora<\/jats:italic>\n                      and a decreased presence of\n                      <jats:italic toggle=\"yes\">Aspergillus<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Penicillium<\/jats:italic>\n                      , and\n                      <jats:italic toggle=\"yes\">Rhodotorula<\/jats:italic>\n                      . In addition,\n                      <jats:italic toggle=\"yes\">Pichia<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Saccharomycopsis<\/jats:italic>\n                      , and\n                      <jats:italic toggle=\"yes\">Cladosporium<\/jats:italic>\n                      were especially enriched in patients without residual CT abnormalities at 2 years. At 2 years post-discharge, significant correlations were observed between pulmonary function and gut mycobiota, including negative correlations between\n                      <jats:italic toggle=\"yes\">Hanseniaspora<\/jats:italic>\n                      and PEF, as well as negative correlations between\n                      <jats:italic toggle=\"yes\">Saturnispora<\/jats:italic>\n                      and DLCO. This study reveals the longitudinal shifts in gut mycobiota over 2 years post-discharge in COVID-19 patients. Significant correlations were observed between pulmonary function and the gut mycobiota, suggesting a potential detrimental effect on lung function, offering potential insights into the pathogenesis of post-acute COVID-19 syndromes.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.03007-24","type":"journal-article","created":{"date-parts":[[2025,5,23]],"date-time":"2025-05-23T09:00:43Z","timestamp":1747990843000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Longitudinal alterations of gut mycobiota during 2 years after COVID-19 and its correlation with pulmonary sequela"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-2255-9866","authenticated-orcid":true,"given":"Qianhan","family":"Xie","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00a2xv884","id-type":"ROR","asserted-by":"publisher"}],"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, 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