Microbiota profiling using stool samples is limited in its ability to represent intestinal microbial dynamics. CRISPR-engineered bacteria can be used to acquire cellular RNAs and create a gene expression ‘memory’ during gastrointestinal transit, with the potential to capture microbial transcriptomic changes in the gastrointestinal tract without invasive sampling.
References
Donaldson, G. P., Lee, S. M. & Mazmanian, S. K. Gut biogeography of the bacterial microbiota. Nat. Rev. Microbiol. 14, 20–32 (2016).
Tropini, C., Earle, K. A., Huang, K. C. & Sonnenburg, J. L. The gut microbiome: connecting spatial organization to function. Cell Host Microbe 21, 433–442 (2017).
Zmora, N. et al. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell 174, 1388–1405.e21 (2018).
Olsson, L. M. et al. Dynamics of the normal gut microbiota: a longitudinal one-year population study in Sweden. Cell Host Microbe 30, 726–739.e3 (2022).
Montassier, E. et al. Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner. Nat. Microbiol. 6, 1043–1054 (2021).
Schmidt, F. et al. Noninvasive assessment of gut function using transcriptional recording sentinel cells. Science 376, eabm6038 (2022).
Schmidt, F., Cherepkova, M. Y. & Platt, R. J. Transcriptional recording by CRISPR spacer acquisition from RNA. Nature 562, 380–385 (2018).
Tanna, T., Schmidt, F., Cherepkova, M. Y., Okoniewski, M. & Platt, R. J. Recording transcriptional histories using Record-seq. Nat. Protoc. 15, 513–539 (2020).
Jin, W.-B. et al. Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome. Cell 185, 547–562.e22 (2022).
Sheth, R. U., Yim, S. S., Wu, F. L. & Wang, H. H. Multiplex recording of cellular events over time on CRISPR biological tape. Science 358, 1457–1461 (2017).
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Crits-Christoph, A., Suez, J. Gut bacteria go on record. Nat Rev Gastroenterol Hepatol 19, 557–558 (2022). https://doi.org/10.1038/s41575-022-00653-3
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DOI: https://doi.org/10.1038/s41575-022-00653-3
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