Technical challenges and high costs remain barriers to the widespread application of microbial single-cell genomics. However, combining meta-omics approaches with single-cell genomics provides new opportunities to better understand microbial diversity, function and community dynamics.
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References
Raghunathan, A. et al. Genomic DNA amplification from a single bacterium. Appl. Environ. Microbiol. 71, 3342â3347 (2005).
Woyke, T., Doud, D. F. R. & Schulz, F. The trajectory of microbial single-cell sequencing. Nat. Methods 14, 1045â1054 (2017).
Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431â437 (2013).
Marcy, Y. et al. Dissecting biological âdark matterâ with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl Acad. Sci. USA 104, 11889â11894 (2007).
Li, Y. et al. Single-cell genomics of rumen ciliates reveals the functional diversity of uncultivated eukaryotes. Nat. Commun. 13, 7032 (2022).
Kashtan, N. et al. Single-cell genomics reveals hundreds of coexisting subpopulations in wild. Prochlorococcus. Science 344, 416â420 (2014).
Shen, Y. et al. High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in human gut microbiome. Protein Cell 16, 211â226 (2024).
Zheng, W. et al. High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome. Science 376, eabm1483 (2022).
Lan, F., Demaree, B., Ahmed, N. & Abate, A. R. Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding. Nat. Biotechnol. 35, 640â646 (2017).
Dodsworth, J. A. et al. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat. Commun. 4, 1854 (2013).
Balaban, N. Q., Merrin, J., Chait, R., Kowalik, L. & Leibler, S. Bacterial persistence as a phenotypic switch. Science 305, 1622â1625 (2004).
Dar, D., Dar, N., Cai, L. & Newman, D. K. Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution. Science 373, eabi4882 (2021).
Engelberts, J. P. et al. GenomeFISH: genome-based fluorescence in situ hybridization for strain-level visualization of microbial communities. ISME J. 19, wraf138 (2025).
Kuchina, A. et al. Microbial single-cell RNA sequencing by split-pool barcoding. Science 371, eaba5257 (2021).
Jia, M. et al. Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome. Nat. Microbiol. 9, 1884â1898 (2024).
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Engelberts, J.P., Tyson, G.W. Understanding microbial ecology and evolution with single-cell genomics. Nat Rev Genet 27, 3â4 (2026). https://doi.org/10.1038/s41576-025-00918-y
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DOI: https://doi.org/10.1038/s41576-025-00918-y