Functional Profiling of the Gut Microbiome from Bulk to Single-Cell: A Pilot Study on Exercise-Induced Effects

Host-adapted microbial communities, or microbiomes, consist of commensal, symbiotic, and pathogenic microorganisms localized to specific body sites. The human gut microbiome, encompassing bacteria, viruses, archaea, and small eukaryotes such as fungi, expresses an estimated 3.3 million genes. These cells play integral roles in human digestion, metabolism, and immune function.\nThis research aims to profile complex microbial communities in human stool samples to understand the potential impact of exercise on gut microbial functionalities. While metatranscriptomics (MT) provides a global view of community gene expression, single-cell RNA (scRNA) profiling identifies transcriptional changes in individual cells, offering insights into phenotypic heterogeneity. Although scRNA profiling of mammalian cells is established, microbial scRNA profiling presents challenges. This work addresses these challenges by testing different permeabilization and rRNA depletion techniques for fragile cells.\nOverall, this research emphasizes the importance of functional profiling of the gut microbiome, advancing approaches for refined profiling with potential biomedical, environmental, food sciences, and synthetic biology applications.