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The Expobiome Map – Exploring the role of microbiome-derived molecules

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Published on Friday, 09 September 2022

The human microbiome, the collection of microorganisms that live in and on our body, is intricately connected to our health. Recent studies have shown that these microbial communities are implicated in various diseases and that the molecules they produce could be drivers of many pathogenic processes including inflammation. However, much remains to be discovered about the biology of the microbiome and its complex interactions with the human host, especially the way by which gut microbiome-derived molecules shape our immune response.

In two papers recently published in the journal Cell Host & Microbe, researchers from the Luxembourg Centre for System Biomedicine (LCSB) and the Department of Life Sciences and Medicine at the University of Luxembourg discuss the gaps in our understanding of the gut microbiome and present the Expobiome Map. This interactive tool compiles the current knowledge about interactions between microbiome-derived molecules and immune pathways. Developed as part of the ERC-funded project ExpoBiome led by Prof. Paul Wilmes, the map allows scientists to visualise and explore the growing body of literature on the topic and, importantly, provides a basis to develop new hypotheses.

The microbiome molecular complex in health and disease

The ecological community of commensal, symbiotic and pathogenic microorganisms that inhabit our digestive tract produces a wide range of molecules. Our organs and tissues are exposed to this group of biomolecules, coined the “expobiome” by the authors of the two articles. They include nucleic acids, peptides, proteins and metabolites, and impact human physiology in multiple ways. 

In health, the gut microbiome confers essential functions, such as digestion and synthesis of vitamins, contributes to metabolism and plays an important role in the regulation of the immune system. On the other hand, perturbations of this microbial community – called dysbiosis – have been reported in several chronic diseases associated with local or systemic inflammation, including neurodegenerative diseases. “It is therefore crucial to better understand the functional implications of changes in the gut microbiome in relation to the immunomodulatory effects of the molecules produced by these microorganisms,” explains Prof. Wilmes, head of the Systems Ecology group at the LCSB.

Visualising a complex network of interactions

This is where the new tool developed by the LCSB researchers comes into play. Host-microbiome interactions involve numerous combinations of molecules which contribute to many different disease processes. To compile the existing knowledge about this complex network and showcase the stimulation of immune pathways by microbiome-derived biomolecules across different diseases, members of the Systems Ecology group, the Bioinformatics Core and the Medical Translational Research group created the Expobiome Map.

“We integrated information from several databases and from the literature in the form of a visual display,” details Dr Velma Aho, member of the Systems Ecology group and co-author of the two papers. The resulting map can be browsed online, allowing the scientific community to easily access details about the source and target elements of interactions, as well as the factors these elements affect and are affected by.

This interactive tool can help users identify knowledge gaps, make inferences on likely links between specific microbes and disease processes, and build novel hypotheses. “It is meant as a way to connect the dots, a basis to contextualise and expand our current understanding of the mechanistic role of the gut microbiome in human health and disease,” concludes Prof. Wilmes.

Check out the Expobiome Map >>

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This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 863664). The work was further supported by the Luxembourg National Research Fund (FNR) CORE/16/BM/11333923 (MiBiPa).