Diagnostic and Therapeutic Use of Microbiota to Soon Become Reality

The microbiome holds promise for diagnostics, such as colon cancer screening and predicting immunotherapy response, as well as for therapeutic uses like microbiota transplants and engineered probiotics. A new article published in Cell outlines a roadmap to bridge these challenges and guide doctors in translating microbiome research into real-world clinical practice.

The article, authored by a team of physician-scientists from Agostino Gemelli University Policlinic (Rome, Italy) and the Catholic University (Milan, Italy), aims to serve as a practical reference for clinicians. It summarizes current knowledge from microbiome studies and outlines how these insights can be applied in diagnostics and treatment. It also addresses the key barriers preventing this progress: a lack of standardization, inadequate clinical trial design, limited large-scale studies, and a cultural gap in clinician familiarity with microbiome science. According to the authors, the microbiome’s diagnostic and therapeutic potential is broad but remains underused due to difficulties in establishing direct causal links between microbiota composition and disease. Variability in individual microbiomes and external factors like diet and medication use complicate clinical study design.

Moreover, there is a lack of harmonized testing protocols, and most studies are single-center and small-scale, restricting wider application. The authors also note a major gap in interdisciplinary communication, which slows translation of lab research into clinical use. However, several promising applications are now approaching clinical viability. In diagnostics, microbiota composition could soon serve as a biomarker for early disease detection, particularly in colon cancer. It may also help distinguish between conditions such as ulcerative colitis and Crohn’s disease or predict a patient’s response to immunotherapy, especially in lung cancer and melanoma. On the therapeutic front, microbiota transplantation—already in use for Clostridium difficile infections—is evolving toward refined microbial cocktails. Other avenues include the use of lytic bacteriophages to target drug-resistant bacteria and engineered probiotics that produce or deliver therapeutic compounds.

To accelerate the adoption of microbiome-based tools, the authors propose several concrete actions: standardizing microbiota test reporting across labs, improving clinical trial design, aligning basic research with clinical needs, and training doctors to interpret and use microbiome data. Among the first expected clinical applications is a colon cancer screening test combining fecal occult blood testing with microbiota analysis to guide decisions about colonoscopy. Similarly, a test to predict cancer immunotherapy response based on microbiota profiles is also nearing readiness for clinical use. On the therapeutic front, future targets include using microbiota to eradicate multidrug-resistant infections such as intestinal Klebsiella, particularly in high-risk patients awaiting organ transplants. Over the long term, microbiome alterations could help boost the effectiveness of immunotherapies in cancer care.

“Despite a huge amount of research and studies on the microbiome, clinical applications are still very scarce, sometimes not entirely orthodox, sometimes “primitive”, said Dr. Gianluca Ianiro, researcher in Gastroenterology at the Catholic University and medical director of the Gastroenterology Unit at the Gemelli IRCCS Polyclinic. “But this will soon change, because the microbiome is the perfect target for precision medicine, specific to each individual and variable in composition depending on life events and diet."