In July, we welcomed participants to the EMBO | EMBL Symposium ‘Metabolic interactions shape ecosystems’ which explored how metabolism shapes ecosystems, promoting cross-disciplinary insight and sustainable system management.

The meeting brought together researchers from diverse fields to examine how metabolic interactions influence the development, resilience and sustainability of biological ecosystems, from holobionts to environmental and engineered systems. By connecting perspectives from disciplines that do not typically meet at the same conference, the symposium fostered the exchange of ideas, approaches and methodologies for understanding complex metabolic networks.

With 52 posters presented on site, participants had many opportunities to share their research and connect with peers. We are delighted to highlight the poster prize winners, whose work showcased the breadth and innovative approaches presented at the meeting. Congratulations Katharina, Hannah, and Anna!

When Homology Fails: Functional Diversity in urocanate reductases

Presenter: Katharina Beck

Authors: Katharina Beck, Gaohua Yang, Fredrik Bäckhed, Chuqing Sun, Wanli He

Abstract:

Host–microbe interactions critically influence human health, yet their mechanistic basis remains poorly understood. Despite rapid growth in metagenomic sequencing data, experimentally validated functional gene annotations lag behind, increasing the risk of misannotations. This is exemplified by urocanate reductase (UrdA), previously misannotated as a fumarate reductase but now recognized for producing the disease-associated metabolite imidazole propionate.

Here, we systematically characterize the catalytic landscape of UrdA homologues using detailed enzyme kinetics, structural analysis, and mutagenesis. We observe substantial variation in substrate affinity and catalytic efficiency, demonstrating that sequence homology or three-dimensional similarity alone are insufficient to predict function. Instead, we identify key amino acid residues within the active site that determine catalytic efficiency and substrate specificity. These residues enable discrimination between bona fide urocanate-reducing enzymes and functionally divergent homologues, despite low overall sequence similarity.

Importantly, homologues with altered active-site composition show reduced urocanate activity but gain efficiency toward alternative substrates, revealing pronounced substrate promiscuity.  Gene induction and competition assays under physiologically relevant substrate conditions confirm that enzyme activity is determined primarily by intrinsic catalytic properties but also by the complexity of the environment.

Together, our findings demonstrate that minimal changes in active-site architecture can reprogram enzyme specificity and thus metabolic output, highlighting the limitations of sequence or structure-based annotation. This work provides a mechanistic framework for improving functional predictions and advances our understanding of how microbial metabolism contributes to host–microbe interactions and disease.

Due to the confidentiality of the unpublished data, we cannot show the poster.

Microbial communities in context: dissecting rhizobiome interactions

Presenter: Hannah Jeckel

Authors: Hannah Jeckel, Reinaldo E. Alcalde, Xiaoyu Shan, Inês B. Trindade, Dianne K. Newman

Abstract:

Microbial communities are ubiquitous on earth and play critical roles in many ecosystems, influencing the health of humans, animals and plants. They commonly consist of a variety of species, sometimes extending across kingdoms, with complex and context-dependent interactions. Predicting, understanding, and even observing these interactions and how they shape the development of a community can be a significant challenge that requires simplified experimental setups which nevertheless capture the essential aspects of the system. Yet it is often unclear what these essential aspects are or how they can be reproduced in a lab environment.

In this presentation I will describe how the experimental environment influences interactions between bacterial strains isolated from wheat rhizospheres, which can lead to dramatic changes in community development between different experimental setups. These changes can be instrumental in revealing which aspects of a system make or break a phenotype. To leverage this, we introduce a succession of experimental setups with increasing complexity that allows us to systematically observe bacterial interactions, identify key parameters shaping these interactions, and link them to the natural context of the rhizosphere.

Focusing on two co-isolated strains whose environment-dependent interactions can be both beneficial (cross-feeding) and antagonistic (secretion of harmful secondary metabolites), we utilize this approach to explore the range of their interactions across systems and shed light onto possible mechanisms of their co-existence in the rhizosphere.

Due to the confidentiality of the unpublished data, we cannot show the poster.

When interactions change: Metabolic feedbacks drive dynamic microbial interactions

Presenter: Anna S. Weiss

Authors: Anna S. Weiss, Megan N.Y. Lee, Stefano Ugolini, Roman Stocker, Olga T. Schubert, Martin Ackermann

Abstract:

Metabolic interactions between microbes are inherently dynamic, emerging from feedbacks between cellular activity and environmental modification. As microbes consume and release metabolites, they continuously reshape their local environment, which in turn alters the nature and strength of interactions. Despite their central role in ecosystem functioning, these feedbacks are rarely resolved in time, limiting our ability to link metabolic processes to ecological outcomes.

Here, we investigate how microbial interactions change over time across environmental contexts. Using a high-throughput microdroplet platform, we quantify time-resolved growth dynamics of bacterial co-cultures across a diverse set of carbon sources. This approach allows us to systematically capture how environmental modification and strain-specific interaction motifs feed back on interspecies dynamics under controlled but ecologically relevant conditions.

Across thousands of conditions, we find that interactions are not fixed properties of species pairs, but shift over time between competitive, neutral, and facilitative regimes. These shifts follow reproducible temporal trajectories that depend on the metabolic context. By integrating these measurements with a consumer-resource model, we explore how differences in growth rates and metabolic strategies influence the emergence and dynamics of interactions across substrates.

Together, our results show that microbial interactions are dynamic processes structured by environmental feedbacks. This work provides a quantitative framework for connecting microbial metabolic interactions to ecological processes and highlights the importance of temporal dynamics for understanding how microbial communities function across environments.

Due to the confidentiality of the unpublished data, we cannot show the poster.

The EMBO | EMBL Symposium ‘Metabolic interactions shape ecosystems‘ took place from 21 – 24 July 2026 at EMBL Heidelberg and virtually.