A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases

The gut microbiome has been implicated in various human diseases, though findings across studies have shown considerable variability. In this study, we reanalyzed 6314 publicly available fecal metagenomes from 36 case-control studies on different diseases to investigate microbial diversity and disease-shared signatures. Using a unified analysis pipeline, we observed reduced microbial diversity in many diseases, while some exhibited increased diversity. Significant alterations in microbial communities were detected across most diseases. A meta-analysis identified 277 disease-associated gut species, including numerous opportunistic pathogens enriched in patients and a higher abundance of protective species in individuals from controls (AUC = 0.825), and high-risk paths inherent in distinguishing disease individuals from controls (AUC = 0.776) and high-risk patients from general cohorts. These results offer insights into the gut microbiome’s role in common diseases and the potential for personalized disease management strategies.