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.

From 2019 to 2024, he was an assistant professor at the Amsterdam University Medical Center returning to the study of human microbiomes with a focus on function, evolution and biology of the human microbiome as well as pathogens with the Laboratory for Applied Evolutionary Biology.

Since 2025, he is a PI and Project Professor at the Keio University Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q) in Tokyo, Japan. There he continues his work on the human microbiome to understand the inner workings of microbial communities and their evolutionary history by using computational approaches to analyze multi-‘omics datasets