Panelists urge standards for microbiome diagnostics and colonization surveillance

Michael Craig of the Centers for Disease Control and Prevention asked the panel how to move from the concept of a 'healthy' microbiome to operational diagnostic definitions. Dr. Ami Bhatt suggested incorporating absolute abundance measures and metabolomic markers: "one way to say that somebody has a healthy microbiome might be to have an absolute abundance or concentration of anaerobes above a certain level," she said. Dr. Katrina Whiteson recommended standards and controls (NIST or commercial fecal standards) to reduce batch effects and make results comparable across labs.

Panelists also discussed practical, accessible readouts—fecal pH and redox potential—as candidate surrogate markers for anaerobic activity, and recommended that pilot surveillance programs consider colonization endpoints (presence or high abundance of known pathogens) in addition to clinical infections. The group emphasized that defining thresholds will require reference standards, multicenter data, and prospective validation.