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Cross-species RNA-seq for deciphering host–microbe interactions

Abstract

The human body is constantly exposed to microorganisms, which entails manifold interactions between human cells and diverse commensal or pathogenic bacteria. The cellular states of the interacting cells are decisive for the outcome of these encounters such as whether bacterial virulence programmes and host defence or tolerance mechanisms are induced. This Review summarizes how next-generation RNA sequencing (RNA-seq) has become a primary technology to study host–microbe interactions with high resolution, improving our understanding of the physiological consequences and the mechanisms at play. We illustrate how the discriminatory power and sensitivity of RNA-seq helps to dissect increasingly complex cellular interactions in time and space down to the single-cell level. We also outline how future transcriptomics may answer currently open questions in host–microbe interactions and inform treatment schemes for microbial disorders.

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Fig. 1: The history of RNA-seq-based infection research.
Fig. 2: Comparison of cellular RNA content between bacteria and mammals.
Fig. 3: The basic steps in commonly used protocols for strand-specific bacterial, mammalian or dual expression profiling.
Fig. 4: Graphical overview of RNA-seq-based approaches to study inter-species interactions in the mammalian intestine.
Fig. 5: Molecular aspects of host–pathogen interactions revealed by transcriptomics.

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Acknowledgements

The authors acknowledge financial support from the German Research Foundation (DFG): Individual Research Grant We6689/1-1 (to A.J.W.) and Leibnitz Award Vo875/18 (to J.V.).

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Glossary

Axenic cultures

Describes cultures comprised of only a single, defined bacterial species or strain.

Gnotobiotic

Pertaining to ‘gnotobiosis’, which is Greek for ‘known life’. The term generally describes biological systems wherein all present organisms can be accounted for. In the present context, the term refers to ex-germ-free mice that were inoculated and colonized with a defined bacterial species or consortium.

Metatranscriptomics

Methods to detect and quantify steady-state transcript levels from multiple bacterial species within a community present in a given environmental or host-derived sample.

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Westermann, A.J., Vogel, J. Cross-species RNA-seq for deciphering host–microbe interactions. Nat Rev Genet 22, 361–378 (2021). https://doi.org/10.1038/s41576-021-00326-y

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