Power of Poop: Identification and Analysis of Gut Microbiome Biomarkers in Diarrhea

The human gut microbiome, a vast collection of billions of bacteria in the gastrointestinal tract, plays a crucial role in maintaining host health through homeostasis. Diarrhea, which affects approximately 179 million people annually, significantly alters the gut microbiome. While infectious diarrhea is characterized by an increase in pathogens such as Escherichia coli, the changes in gut microbiome following non-infectious and chronic diarrhea remain unclear. Recent advances in metagenomic sequencing have enabled us to investigate the changes in gut microbiome. To identify biomarkers in diarrhea and characterize the gut microbiome, we integrated datasets from 12 published studies into a comprehensive dataset, comprising 1015 healthy samples and 2302 diarrhea-related disease samples, among which approximately 90% are non-infectious. Using linear regression model and machine learning, we identified microbial taxa enriched in healthy samples, including Bacteroides uniformis, Bacteroides vulgatus, Akkermansia muciniphila, Firmicutes bacterium, and Alistipes. In contrast, Flavonifractor plautii, E. coli, and Prevotella were more abundant and prevalent in diarrhea samples. For microbial function analysis, we found that pathways such as phytol degradation and aerobic respiration I (cytochrome C) were enriched in healthy samples, whereas other pathways including glycerol degradation, methanogenesis, isoprene biosynthesis, and taxadiene biosynthesis, were more commonly detected in diarrhea samples. We employed graph theory and inferred a denser but less stable network from diarrhea samples compared to the network of healthy controls. These results indicate that healthy and diarrhea gut microbiomes have distinct features characterizing diarrhea alterations. We anticipate that these biomarkers can be used for personalized dietary interventions and targeted, cost-effective diagnosis and treatments of diarrhea that consider complex gut microbiome interactions.