Single-Cell Transcriptomics for Microbial Communities

Single-cell transcriptomics is reshaping microbiome research by moving beyond bulk profiling to capture the activity of individual microbes. This shift reveals functional heterogeneity within communities, including differences in metabolism, antibiotic responses, and gene exchange—patterns that remain hidden in population-level analyses.

New methods for microbial cell capture and RNA analysis are making it possible to dissect gut microbiota, resistance mechanisms, and the dynamics of mobile genetic elements. Despite technical hurdles such as low RNA yield and tough cell walls, the approach is advancing quickly and promises to become essential for understanding microbial roles in health, disease, and the environment.

(A) Microbiomes are interactive, multispecies communities, but bulk analysis obscures functional diversification among cells of the same species, arising from environmental and genetic heterogeneity. (B) The schematic dimensional reduction plots indicate how subpopulations are identified according to their gene expression profiles. Single-cell transcriptomics can help to reveal functional aspects of this heterogeneity and dissect microbial ecosystems at cellular resolution.

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https://www.science.org/doi/10.1126/science.adp6252