New ultrasensitive assay to measure host immune profile from feces

Immune activity is often profiled using blood or tissue samples, which is invasive and difficult to scale. Dense, noninvasive access to the gut immune system is necessary to understand gut microbiome-immune crosstalk. Fecal matter has been used to profile gut immune status using a few high abundance markers like calprotectin and eosinophil derived neurotoxin. But, low abundance proteins (including cytokines) which offer a detailed view into immune activity have been difficult to detect in feces using existing methods, particularly in the absence of inflammation. We present a new ultrasensitive fecal assay that profiles immune proteins at femtomolar levels, providing an unprecedented window into gut immune activity. We are able to quantitate cytokine levels in not only healthy conventional but also germ-free mice. Ongoing work is studying the link between cytokine levels in feces, gut tissue, and peripheral blood. Our assay will be used to generate data to train machine learning models of immune-microbiome dynamics. We anticipate that the assay can be used for diagnostic purposes in the future, aiding in the transition to personalized precision medicine.