Beyond dysbiosis: Reframing microbiome-associated diseases from taxonomy to functional and ecological models

Dysbiosis is widely used to describe disease-associated alterations of the gut microbiome.It has been linked to the occurrence of many diseases, including inflammatory bowel disease, irritable bowel syndrome, colorectal cancer, and metabolic dysfunctionassociated steatotic liver disease.Despite its widespread use, dysbiosis remains poorly defined and therefore has limited scientific utility.The key issues are: The absence of a universal healthy reference state, conflation of correlation with causation, overemphasis on microbial taxonomy over its function, neglect of ecological interactions, and inadequate integration with host biology.Here, we critically examine these limitations and propose five complementary, measurable dimensions: Functional, metabolic, ecological, network, and host-microbiome dysbiosis.We integrate these dimensions into a six-level framework linking gene-environment factors, microbial ecology, community function, metabolite output, host response, and disease phenotype.Each dimension is linked to appropriate assays and an explicit falsification criterion.We then examine how this framework could inform microbiome modulation strategy for precision medicine.Reframing dysbiosis as a set of measurable, falsifiable disturbances rather than a generic taxonomic imbalance may improve mechanistic inference and clinical translation.