The trillions of microorganisms living in our intestine influence our health, from digestion and metabolism to immunity. Yet scientists still struggle to understand how these microbes shape these important physiological functions because gut microbiomes are extraordinarily complex, redundant, and dynamic. New technologies are therefore essential for advancing microbiome research. Researchers at the University of Vienna have now reported effective strategies for simultaneously measuring thousands of microbial and host proteins. The findings have been published in Nature Communications.