Univ.-Prof. Dr. David Berry

Professor at the Division of Microbial Ecology

☎ +43 1 4277 91212
✉ david.berry(at)univie.ac.at

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Research in David Berry’s group is focused on understanding the biology of the human microbiota and its role in health and disease. He has pioneered the development of novel experimental and computational tools to reveal the functionof microbial communities and has developed single cell isotope labelling techniques to characterise functional guilds in the intestinal ecosystem.

The main research aims of David’s group are to gain a fundamental understanding of the assembly and interactions of the intestinal microbiota and to uncover how the microbiota affects host physiology. David is active in translational and clinical research in several fields, including chronic inflammation, nutrition, metabolic syndrome, cancer, and gut-immune-brain axis development in newborns. He is coordinator of an Austrian Science Fund (FWF) research consortium focused on premature infant health (2023).

Research Topics

Physiology and ecology of the gut microbiota

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).

Translational microbiome research

The human microbiome has recently emerged as a critical factor in health and disease and is now recognized to be play key roles in development, nutrition, immunological function, metabolic health, and neurological processes. The microbiome has been associated with myriad conditions ranging from infectious diseases to chronic illnesses and can influence disease susceptibility and progression as well as therapeutic outcomes. The prognostic and diagnostic value of microbiome profiling has become increasingly recognized, and microbiome-targeted interventions and microbiome-derived small molecules hold promise for novel therapeutic strategies. We are active in researching the human microbiota in a variety of medically relevant contexts, such as inflammatory bowel diseases, cancer, atopic dermatitis (Pruritis project), dietary mycotoxin exposure (MycoGut project), and development of the gut microbiota-immune-brain axis in extremely premature infants (NeoGIBA project).

Single cell stable isotope probing of microbial communities

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 (Pereiraet 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).

Research Projects

Gut-immune-brain axis dysfunction in premature neonates: Molecular mechanisms and long-term consequences (NeoGIBA)

Current Projects DOME

Extremely premature infants, which are born before the 28th week of gestation and weighing <1,000 grams, are a highly vulnerable patient group. They…

The Premature Gut Microbiome And The Influence On Neonatal Immunity, Brain Development And White Matter Injury - The Premibrain Study

Past Projects DOME

Recent advances in neonatal intensive care have dramatically increased the survival rate of extremely premature infants but the number of survivors…

Illuminating Functional Networks And Keystone Species In The Gut (Funkeygut)

Past Projects DOME

The human intestine is home to a complex microbial ecosystem important to nutrition and health. In recent years molecular and bioinformatics tools…

Public Outreach

I serve as a scientific advisor for the start-up microbiome analysis company Biome Diagnostics GmbH and am on the scientific advisory board of the Austrian Microbiome Initiative (AMICI) and advisory board of the Austrian Society for Hygiene, Microbiology and Preventive Medicine (ÖGHMP). I am active in outreach to the general public in the form of lectures, panel discussions, and interviews. I lead the project “Fibers, Microbiology and Cooking” (BaMiKo project) to increase public awareness of the importance of nutrition to support a healthy microbiome. Additionally, I am engaged in collaborations with artists in the area of “BioArt” in order to increase awareness among the public about biology and biotechnology. This has resulted in several public presentations and performances such as “Co-Corporeality - interactive spaces in the era of biomediality”. (https://cocorporeality.net/), publications, and a teaching workshop at the University of Arts, Berlin (Co-taught with Lucie Strecker).