Microbiome dysbiosis in long COVID: a scoping review of mechanistic insights, symptom associations, and therapeutic targets

The human microbiome, particularly the gut microbiome, plays a critical role in host immunity, metabolism, and barrier function. Emerging evidence suggests that persistent alterations in microbiome composition—termed dysbiosis—may contribute to the development and symptom persistence of Long COVID. To map the available literature on microbiome dysbiosis in relation to Long COVID, identify key microbial alterations, associated symptoms, and evaluate potential microbiome-targeted interventions. The scoping review followed Joanna Briggs Institute (JBI) methodological guidance and was reported according to PRISMA-ScR. A comprehensive search of PubMed, Scopus, Web of Science, and Cochrane Library databases was conducted for studies published from January 2000 to May 2025. Eligible studies included human subjects with a clinical diagnosis of Long COVID and microbiome-related outcomes. Data was charted using a standardized form and synthesized narratively and descriptively. A total of 62 sources were included, most of which were narrative, conceptual, or descriptive in nature. The available literature most frequently discussed gut microbiome dysbiosis in relation to Long COVID, including reduced abundance of beneficial taxa such as Faecalibacterium prausnitzii and Bifidobacterium adolescentis , and increased abundance of opportunistic or pro-inflammatory taxa such as Ruminococcus gnavus and Clostridium innocuum . Reported or proposed associations involved fatigue, gastrointestinal symptoms, neuropsychiatric manifestations, and immune dysregulation. Evidence from respiratory and oral microbiomes was more limited. Microbiome-targeted interventions, including probiotics, prebiotics, synbiotics, diet, and fecal microbiota transplantation (FMT), were mainly proposed or discussed, with limited direct interventional evidence. Current evidence suggests that microbiome alterations may be associated with Long COVID, but the available literature remains largely descriptive, observational, and hypothesis-generating. Further longitudinal and interventional studies are needed to clarify causality and determine whether microbiome-targeted strategies have therapeutic value.