Daniel Mende studied bioinformatics at the University of Frankfurt (Germany) before moving to the European Molecular Biology Laboratory in Heidelberg (Germany) for his PhD studies with Peer Bork (2009-2013) with a focus on the human microbiome and the development of methods for its analysis.

For his postdoctoral studies, Daniel moved to the University of Hawaii to work with Ed DeLong on microbial communities in the Oceans in 2014.

In 2019, he started his own research group at the Amsterdam UMC studying the role, evolution and biology of the human microbiome as well as pathogens with the Laboratory for Applied Evolutionary Biology.