The Human Microbiome in Healthcare: Ecological Mechanisms, Disease Associations and Evidence-Based Clinical Translation

Abstract

The purpose: Microorganisms live in the human body and impact the ecology of the mucous membranes, host metabolism, and immune regulation; however, the clinical relevance of the variation of the human microbiome varies greatly among diseases. This review critically analyzes the oral and intestinal microbiome biology, clinical links, measurement challenges and therapeutic evidence. Methods: The foundational studies, mechanistic studies, randomized trials, regulatory documents, or practice guidelines were purposively selected up to October 2026 for a critical narrative review. Findings: Oral and intestinal microbial communities are site-specific, functionally diverse, and their composition is changed by inflammation, antibiotics, diet, and other exposures to the host, making causal interpretation difficult. Microbial associations have been consistently found in both periodontitis and inflammatory bowel disease, but for the individual, microbiome testing is not frequently used to guide treatment. Strain resolved analyses indicate that specific Fusobacterium nucleatum strains are involved in colorectal cancer pathogenesis, but there is no routine clinical use. There is a well-defined indication for using microbiota-based interventions in adults for the prevention of recurrent C. difficile infection in cases where the patients are appropriately selected, and it is still investigational in other gastrointestinal disorders. Implications: Clinical translation requires prospective validation, reproducible multi-omics measurement, transparent reporting, clinically meaningful outcomes and careful assessment of infectious risk. Microbial associations should not be presented as evidence that modifying the microbiome will improve disease outcomes. Additional materials: The article contains one table and 14 references.