Professor at the Division of Microbial Ecology

☎ +43 1 4277 91212

✉ david.berry@univie.ac.at

Deciphering microbial interactions and detecting keystone species with co-occurrence networks.

Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members, thoughmany questions remain about their validity and performance. Using a simulation-based approach, we evaluated how well networks reveal underlying interactions. We found that co-occurrence networks can recapitulate interaction networks under certain conditions, and also identified topological features associated with keystone species in co-occurrence networks. This work provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets. (Berry and Widder, 2014)

Single cell stable isotope probing of the gut microbiota

Microbes live almost exclusively in complex communities, and it remains a major challenge to identify the activity of microbial cells under natural conditions. We have developed tools based on single cell stable isotope probing to address this. Using fluorescence in situ hybridization combined with high-resolution secondary ion mass spectrometry (NanoSIMS) we were able to identify microbial cells that had degraded secreted mucosal proteins (Berry et al., 2013). Recently, we were able to use heavy water as a universal activity marker combined with Raman microspectroscopy to profile the in situ activity of two mucus-degrading species, Akkermansia muciniphila and Bacteroides acidifaciens, to a range of amended nutrients (Berry et al., 2015).