Clinical Recommendations Based on Microbiome Testing
Microbiome testing should not be used to guide clinical treatment decisions outside of research protocols, as the methodology lacks standardization and results cannot be reliably interpreted for individual patient care. 1
Current State of Microbiome Testing
The fundamental limitation is clear: while the microbiome undoubtedly influences human health, commercial testing has not reached clinical utility. An international expert panel explicitly concluded that therapeutic counseling based on microbiome test results is strongly discouraged, as interpretation regarding individual health remains insufficiently conclusive. 1
Why Microbiome Tests Cannot Guide Treatment
Lack of standardization: The methodology for analyzing microbiome composition has not been standardized across laboratories or platforms, making results incomparable and unreliable for clinical decisions. 1
Insufficient clinical validation: Current microbiome tests do not provide value in clinical decision-making given the present state of knowledge and technology. 2
Contamination concerns: Most clinical samples (skin, tissue, blood, urine) are low microbial biomass samples that are extremely vulnerable to contamination from DNA extraction kits, laboratory environments, and handling procedures, leading to false assessments. 3, 4
No established reference ranges: Unlike standard laboratory tests, there are no validated "normal" or "pathological" microbiome profiles that can guide treatment for most conditions. 2
Limited Exceptions Where Microbiome-Based Therapy Has Evidence
Fecal Microbiota Transplantation (FMT)
The only microbiome-based intervention with strong clinical evidence is FMT for specific indications:
Recommended uses:
- Recurrent Clostridioides difficile infection (CDI) after standard antibiotic therapy failure 3
Not recommended (use only in clinical trials):
The AGA explicitly states that conventional FMT should be used outside these narrow indications only within clinical trial contexts. 3
What to Tell Patients Who Present With Microbiome Test Results
Direct Communication Strategy
Explain that while the microbiome is genuinely important for health, commercial testing cannot currently:
- Diagnose specific diseases 2, 1
- Predict disease risk reliably 2
- Guide dietary or supplement recommendations 1
- Determine probiotic selection 1
Evidence-Based Alternatives
Instead of acting on microbiome test results, focus on:
For gastrointestinal symptoms:
- Obtain standard diagnostic workup including culture-based testing when infection is suspected 3
- Use validated clinical criteria (Rome IV for IBS, endoscopy for IBD) 3
- Consider empiric probiotic therapy only in specific contexts (critical illness, antibiotic-associated diarrhea) where meta-analyses show benefit 3
For suspected C. difficile:
- Use validated multistep algorithms combining PCR with toxin enzyme immunoassay, not microbiome profiling 5
- Start empiric treatment based on clinical criteria (recent antibiotics + diarrhea + leukocytosis), not microbiome composition 5
Critical Pitfalls to Avoid
Do not prescribe probiotics, prebiotics, or dietary changes based solely on microbiome test results showing "dysbiosis" or specific bacterial ratios. 1
Do not order repeat microbiome testing to monitor treatment response, as test-to-test variability exceeds meaningful biological changes. 3
Do not interpret low abundance of "beneficial" bacteria or high abundance of "pathogenic" bacteria as diagnostic, since contamination in low-biomass samples creates false signals. 3, 4
Future Considerations
Considerable research remains before microbiome diagnostics can be integrated into clinical care. 2 Current limitations include unresolved issues with compositional data analysis, lack of consensus on statistical models, and inability to distinguish causation from correlation in microbiome-disease associations. 3
Until standardized protocols, validated reference databases, and prospective clinical trials demonstrate clinical utility, microbiome testing should be confined to research settings where proper controls, validation cohorts, and rigorous methodology can be applied. 3