SRS-FISH: a platform to link microbiome function to identity

Microbial communities are the foundation of the biosphere and essential for human health. A mechanistic understanding of microbiomes requires methods to decrypt their composition and function with single cell resolution. The combination of stable isotope probing and fluorescence in situ hybridization (FISH) is widely used for this purpose. However, due to low throughput all available approaches are insufficient for an encompassing understanding of these often highly complex communities. We developed a next generation Raman-FISH platform with a throughput increased by two to three orders of magnitude and applied it to obtain new insights of the contribution of more than 30,000 cells in the human gut microbiome to mucosal sugar degradation - a microbiome function with major importance for human health. Sequencing was performed at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna under the project ID JMF-2110-18.