Gut microbiome composition and dynamics in hospitalized COVID-19 patients and patients with the post-acute COVID-19 syndrome
The gut microbiome plays a pivotal role in the modulation of host responses during viral infections, and recent studies have underscored its significance in the context of COVID-19. We aimed to investigate the dynamics and compositional changes in the gut microbiota of COVID-19 patients, addressing both the acute phase and the recovery process, with a particular focus on the emergence of long COVID-related complications. Involving 146 COVID-19 patients and 110 healthy controls, this study employed a shotgun metagenomics approach for both longitudinal and cross-sectional analyses. Follow-up assessments were conducted at one and three months post-recruitment. We observed a decline in taxonomic diversity among acute, hospitalized COVID-19 patients compared to healthy controls, followed by an increase during the recovery process. A notable contribution of Enterococcus faecium was identified in the acute phase of the infection, accompanied by an increasing abundance of butyrate-producing bacteria (e.g., Roseburia, Lachnospiraceae_unclassified) during the recovery period. We highlighted a protective role of the Prevotella genus in the long-term recovery process, suggesting potential population-specificity in the gut microbiota markers of post-acute COVID-19 syndrome. Our study represents distinctive gut microbiome signatures in COVID-19, with potential diagnostic and prognostic implications, supporting the development of microbiome-based treatment strategies in managing COVID-19 outcomes.