University of Vienna: Decoding the gut microbiome's symphony in health and disease
Researchers at the University of Vienna have developed and evaluated new analytical strategies that enable the simultaneous measurement of thousands of microbial and host proteins, providing deeper insights into how the gut microbiome functions in health and disease. The findings, published in Nature Communications, represent an important step towards a better understanding of the dynamic interactions between intestinal microorganisms and their human host.
Improving future microbiome research
The trillions of microorganisms inhabiting the human intestine influence numerous physiological processes, including digestion, metabolism and immune function. While modern DNA sequencing technologies have revolutionised microbiome research by identifying which microorganisms are present and which functions they could potentially perform, DNA alone cannot reveal which biological activities are actually taking place.
Proteins provide this missing layer of information by revealing which microbial functions are active, how different members of the microbiome contribute to these functions and how the host responds. In the study, researchers systematically compared five state-of-the-art mass spectrometry approaches using human faecal samples to determine which methods offer the highest sensitivity, reproducibility and functional insight.
The work was carried out through a collaboration between the University of Vienna Bruker Daltonics Center of Excellence for Metaproteomics and the Systems Biology of Pain Laboratory within the Division of Pharmacology & Toxicology at the University of Vienna.
According to first author Feng Xian, metaproteomics makes it possible to observe what microbial communities are actually doing rather than simply identifying which microorganisms are present. By establishing the most suitable analytical strategies, the researchers aim to make future microbiome research more sensitive, reproducible and broadly applicable across medicine, environmental science and biotechnology.
From technical developments to clinical insights
The researchers also evaluated the new analytical strategies in a biologically relevant setting by measuring microbial and host proteins throughout disease progression and recovery. The analyses revealed coordinated changes in microbial functions alongside the host's repair response. The best-performing methods consistently captured both microbial activity and host responses during the onset and recovery of intestinal inflammation, demonstrating that methodological improvements can directly translate into meaningful biological insights.
David Gomez-Varela, Director of the Bruker Daltonics Center of Excellence for Metaproteomics, emphasised that improved technologies are essential for addressing the next generation of microbiome research questions. By understanding the molecular activities of microbial communities and the corresponding responses of the host, researchers hope to gain a much deeper understanding of the microbiome's role in human health. The newly established approaches are already being applied in international clinical collaborations investigating the role of microbiomes in neurological, metabolic and autoimmune diseases.