Cross-species RNA-seq for Deciphering Host-microbe Interactions

Overview

Journal Nat Rev Genet

Specialty Genetics

Date 2021 Feb 18

PMID 33597744

Citations 44

Authors

Alexander J Westermann

Jorg Vogel

Affiliations

Soon will be listed here.

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.

Citing Articles

Comparative Transcriptomics Analysis of Foot-and-Mouth Disease Virus-Infected Cell Model Systems.

Ma H, Zheng Z, Liu M, Zhang M, Qu X, Ren J Vet Sci. 2025; 12(2).

PMID: 40005867 PMC: 11860336. DOI: 10.3390/vetsci12020107.

Transcriptional Systems Vaccinology Approaches for Vaccine Adjuvant Profiling.

Pellegrina D, Wilson H, Mutwiri G, Helmy M Vaccines (Basel). 2025; 13(1.

PMID: 39852812 PMC: 11768747. DOI: 10.3390/vaccines13010033.

Understanding the Impact of Salt Stress on Plant Pathogens Through Phenotypic and Transcriptomic Analysis.

Jung H, Han G, Lee D, Jung H, Kim Y, Kong H Plants (Basel). 2025; 14(1.

PMID: 39795357 PMC: 11722782. DOI: 10.3390/plants14010097.

Advances and applications in single-cell and spatial genomics.

Wang J, Ye F, Chai H, Jiang Y, Wang T, Ran X Sci China Life Sci. 2025; .

PMID: 39792333 DOI: 10.1007/s11427-024-2770-x.

Central Taxa Are Keystone Microbes During Early Succession.

Rawstern A, Hernandez D, Afkhami M Ecol Lett. 2024; 28(1):e70031.

PMID: 39737770 PMC: 11687413. DOI: 10.1111/ele.70031.

References

Bumann D . Heterogeneous host-pathogen encounters: act locally, think globally. Cell Host Microbe. 2015; 17(1):13-9. DOI: 10.1016/j.chom.2014.12.006. View

Sarkar S, Heise M . Mouse Models as Resources for Studying Infectious Diseases. Clin Ther. 2019; 41(10):1912-1922. PMC: 7112552. DOI: 10.1016/j.clinthera.2019.08.010. View

Barrila J, Crabbe A, Yang J, Franco K, Nydam S, Forsyth R . Modeling Host-Pathogen Interactions in the Context of the Microenvironment: Three-Dimensional Cell Culture Comes of Age. Infect Immun. 2018; 86(11). PMC: 6204695. DOI: 10.1128/IAI.00282-18. View

Colgan A, Cameron A, Kroger C . If it transcribes, we can sequence it: mining the complexities of host-pathogen-environment interactions using RNA-seq. Curr Opin Microbiol. 2017; 36:37-46. DOI: 10.1016/j.mib.2017.01.010. View

Westermann A, Gorski S, Vogel J . Dual RNA-seq of pathogen and host. Nat Rev Microbiol. 2012; 10(9):618-30. DOI: 10.1038/nrmicro2852. View

Eulalio A, Schulte L, Vogel J . The mammalian microRNA response to bacterial infections. RNA Biol. 2012; 9(6):742-50. DOI: 10.4161/rna.20018. View

Agliano F, Rathinam V, Medvedev A, Vanaja S, Vella A . Long Noncoding RNAs in Host-Pathogen Interactions. Trends Immunol. 2019; 40(6):492-510. PMC: 6556373. DOI: 10.1016/j.it.2019.04.001. View

Westermann A . Regulatory RNAs in Virulence and Host-Microbe Interactions. Microbiol Spectr. 2018; 6(4). PMC: 11633609. DOI: 10.1128/microbiolspec.RWR-0002-2017. View

Saliba A, Westermann A, Gorski S, Vogel J . Single-cell RNA-seq: advances and future challenges. Nucleic Acids Res. 2014; 42(14):8845-60. PMC: 4132710. DOI: 10.1093/nar/gku555. View

10.

Penaranda C, Hung D . Single-Cell RNA Sequencing to Understand Host-Pathogen Interactions. ACS Infect Dis. 2019; 5(3):336-344. DOI: 10.1021/acsinfecdis.8b00369. View

11.

Dreyfus M, Regnier P . The poly(A) tail of mRNAs: bodyguard in eukaryotes, scavenger in bacteria. Cell. 2002; 111(5):611-3. DOI: 10.1016/s0092-8674(02)01137-6. View

12.

Wolin S, Steitz J . Genes for two small cytoplasmic Ro RNAs are adjacent and appear to be single-copy in the human genome. Cell. 1983; 32(3):735-44. DOI: 10.1016/0092-8674(83)90059-4. View

13.

Sim S, Wolin S . Bacterial Y RNAs: Gates, Tethers, and tRNA Mimics. Microbiol Spectr. 2018; 6(4). PMC: 6047535. DOI: 10.1128/microbiolspec.RWR-0023-2018. View

14.

Lundblad E, Altman S . Inhibition of gene expression by RNase P. N Biotechnol. 2010; 27(3):212-21. DOI: 10.1016/j.nbt.2010.03.003. View

15.

Kroger C, Colgan A, Srikumar S, Handler K, Sivasankaran S, Hammarlof D . An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium. Cell Host Microbe. 2013; 14(6):683-95. DOI: 10.1016/j.chom.2013.11.010. View

16.

Hor J, Matera G, Vogel J, Gottesman S, Storz G . Trans-Acting Small RNAs and Their Effects on Gene Expression in and . EcoSal Plus. 2020; 9(1). PMC: 7112153. DOI: 10.1128/ecosalplus.ESP-0030-2019. View

17.

Rion N, Ruegg M . LncRNA-encoded peptides: More than translational noise?. Cell Res. 2017; 27(5):604-605. PMC: 5520851. DOI: 10.1038/cr.2017.35. View

18.

Yao R, Wang Y, Chen L . Cellular functions of long noncoding RNAs. Nat Cell Biol. 2019; 21(5):542-551. DOI: 10.1038/s41556-019-0311-8. View

19.

Stark R, Grzelak M, Hadfield J . RNA sequencing: the teenage years. Nat Rev Genet. 2019; 20(11):631-656. DOI: 10.1038/s41576-019-0150-2. View

20.

van Dijk E, Jaszczyszyn Y, Naquin D, Thermes C . The Third Revolution in Sequencing Technology. Trends Genet. 2018; 34(9):666-681. DOI: 10.1016/j.tig.2018.05.008. View