Jens Walter is Professor of Ecology, Food and the Microbiome at University College Cork and a Principal Investigator at APC Microbiome Ireland. He trained in food science and microbiology at the University of Hohenheim, Germany, before undertaking postdoctoral research in New Zealand and the United States.

He began his independent career at the University of Nebraska–Lincoln and later moved to the University of Alberta, Canada, where he held a Campus Alberta Innovates Program (CAIP) Chair, before relocating to Ireland. He is currently supported by a Science Foundation Ireland Research Professorship.

His research lies at the interface of evolutionary ecology of the gut microbiome and human nutrition, and he is internationally recognized for integrating ecological and evolutionary principles with controlled human studies to understand and modulate the gut microbiome. His work has advanced dietary and microbial strategies for microbiome modulation, including the development of the Non-Industrialized Microbiome (NiMe) diet.

Walter has published over 200 peer-reviewed articles and is consistently ranked among the world’s most highly cited researchers. He has also contributed to shaping debate in the field through influential commentaries challenging prevailing assumptions on causality, prebiotics, experimental models, and the concept of a prenatal microbiome.

His research programme focuses on how ecological and evolutionary forces shape the gut microbiome and how these insights can be used for its modulation. His early work examined the evolution of gut microbes, using Limosilactobacillus reuteri as a model for host specialization and microbe–host co-evolution. This was followed by ecological studies on how host genetics, colonisation history (priority effects), and microbial dispersal govern microbiome assembly, stability, and competitive interactions.

Building on this foundation, his research has increasingly focused on predicting and manipulating microbiome responses to intervention. His group has conducted more than a dozen controlled human studies investigating dietary fibres, prebiotics, whole diets, probiotics, faecal microbiota transplantation, and synbiotic approaches, linking microbiome changes to microbial metabolism and host metabolic and inflammatory outcomes. This includes work showing how discrete fibre structures direct microbial metabolic outputs and how dietary patterns induce coordinated microbiome shifts associated with health.

This work has culminated in the development of the Non-Industrialized Microbiome (NiMe) diet, a strategy grounded in evolutionary and ecological principles and inspired by traditional diets, designed to restore microbiome functions diminished by industrialisation. In parallel, Prof. Walter has helped shape the field through critical evaluation of key concepts, challenging assumptions around causality, prebiotics, experimental models, and the existence of a prenatal microbiome.