Univ.-Prof. Dr. David Berry

The gut microbiota is a diverse community of microorganisms critical for human health. Members of this community cooperate and compete with each other in many ways, and the sum of these interactions determines the composition and function of the microbiota. We employ cutting-edge computational and experimental approaches to predict and elucidate these interspecies interactions. We have used network-based analyses to evaluate properties of keystone species in the microbiota (Berry and Widder, 2014, Bauchinger et al 2024), and are currently developing ensemble modeling approaches, including community-scale metabolic modeling and machine learning, to determine how interactions support the metabolic output of the microbiota (EnhanceFun project). Experimental techniques to identify interspecies interactions include Raman-based sorting and physiological analysis of microbes active in specific nutrient utilization niches and construction of synthetic communities derived from natural communities (Riva et al 2023, Rasoulimehrabani et al 2025, CoE project).

Microbes live almost exclusively in complex communities, and it remains a major challenge to identify the activity of microbial cells under natural conditions. Isotope-based tools are a powerful complement to sequencing-based methods to gain insights into the microbiota (Alcombri et al. 2022). We have developed ex and in vivo stable isotope probing techniques and have established heavy water as a universal cellular activity marker (Berry et al., 2015), which has been adopted by many other research groups worldwide. Deuterium incorporation by active cells can be easily measured using Raman microspectroscopy, a non-destructive technique that allows for post-measurement analysis of single cells (Soo Lee et al., 2019). We have used this approach to identify gut bacteria that use mucus-derived sugars, which are important nutrients for enteric pathogens such as Clostridioides difficile (Pereira et al., 2020), as well as to study the gut species supported by variety of dietary components (Riva et al 2023, Rasoulimehrabani et al 2025, CoE project).