Gastrointestinal symptoms of long COVID relate to the ectopic colonization of specific bacteria that move between the upper and lower alimentary tract

We prospectively collected oral, fecal, and serum samples from 983 antibiotic treatment-naive patients with mild COVID-19 and performed a 3-month follow-up postdischarge. Forty five and 25 paired fecal and saliva samples were collected from these patients at the 3 month follow up and from healthy controls, respectively. Shotgun metagenomic sequencing of fecal samples and 2bRAD sequencing for Microbiome (2bRAD-M) analysis of saliva samples collected from the 45 patients during hospitalization and after 3 months and from healthy controls were performed.