Post-COVID Impairment Phenotyping and Outcomes [Post-CIPO] study
This dataset includes 16S rRNA sequencing profiles from saliva and stool samples collected as part of a prospective cohort study investigating microbiome changes associated with Long COVID. The study enrolled 349 adults from the Post-COVID Impairment Phenotyping and Outcomes (Post-CIPO) cohort. Participants were grouped into three symptom subphenotypes identified via latent class analysis of self-reported symptoms. Microbiome analysis revealed distinct differences in beta diversity across symptom clusters. Specific taxa in saliva, such as *Veillonella* and *Prevotella*, were associated with throat pain, while in stool, *Subdoligranulum* and *Faecalibacterium* were inversely linked to abdominal symptoms. These findings suggest potential microbiome dysbiosis in relation to Long COVID clinical features, independent of viral RNA detection in saliva (5.8%) or stool (1.0%). The dataset provides valuable insights into the microbiome's role in Long COVID and supports further research into microbiome-targeted therapeutic strategies.