Enterohemorrhagic Escherichia coli responds to gut microbiota metabolites by altering metabolism and activating stress responses

ABSTRACT

Enterohemorrhagic Escherichia coli (EHEC) is a major cause of severe bloody diarrhea, with potentially lethal complications, such as hemolytic uremic syndrome. In humans, EHEC colonizes the colon, which is also home to a diverse community of trillions of microbes known as the gut microbiota. Although these microbes and the metabolites that they produce represent an important component of EHEC’s ecological niche, little is known about how EHEC senses and responds to the presence of gut microbiota metabolites. In this study, we used a combined RNA-Seq and Tn-Seq approach to characterize EHEC’s response to metabolites from an in vitro culture of 33 human gut microbiota isolates (MET-1), previously demonstrated to effectively resolve recurrent Clostridioides difficile infection in human patients. Collectively, the results revealed that EHEC adjusts to growth in the presence of microbiota metabolites in two major ways: by altering its metabolism and by activating stress responses. Metabolic adaptations to the presence of microbiota metabolites included increased expression of systems for maintaining redox balance and decreased expression of biotin biosynthesis genes, reflecting the high levels of biotin released by the microbiota into the culture medium. In addition, numerous genes related to envelope and oxidative stress responses (including cpxP, spy, soxS, yhcN, and bhsA) were upregulated during EHEC growth in a medium containing microbiota metabolites. Together, these results provide insight into the molecular mechanisms by which pathogens adapt to the presence of competing microbes in the host environment, which ultimately may enable the development of therapies to enhance colonization resistance and prevent infection.

KEYWORDS:

• Enterohemorrhagic Escherichia coli
• EHEC
• gut microbiota
• metabolites
• RNA-seq
• Tn-seq
• bacterial metabolism
• stress response

Acknowledgments

We are grateful to Tracy Raivio (University of Alberta) for sharing the pJW15 luminescence reporter plasmid and to Matthew Mulvey (University of Utah) for sharing the pSAM-Ec transposon donor plasmid. We would like to thank Wanyin Deng for his valuable feedback on the manuscript. S.L.V. was the recipient of a Killam Postdoctoral Research Fellowship, a Michael Smith Foundation for Health Research Postdoctoral Fellowship, and a CIHR Postdoctoral Fellowship. A.S.P was the recipient of a CIHR Postdoctoral Fellowship [MFE-164659]. B.B.F. is a University of British Columbia Peter Wall Distinguished Professor.

Disclosure statement

No potential conflict of interest was reported by the authors.

Author contributions

S.L.V, A.S.P., B.B.F. designed the study. M.C.D. and E.A.V. prepared and provided materials for the study. S.L.V., A.S.P., A.S.S., L.V.B. designed and performed the in vitro experiments. S.L.V., A.S.P., S.E.W. conducted the animal experiments. S.L.V., S.P.W.V. performed the bioinformatics analyses. S.L.V., A.S.P., S.E.W. performed the data analysis. S.L.V, A.S.P., S.E.W., A.S.S., S.P.W.V., M.C.D., L.V.B., A.J.G., D.J.M., E.A.V., B.B.F. discussed the data and wrote the manuscript. E. A.-V. is co-founder and CSO of NuBiyota, a company seeking to create ‘microbial ecosystem therapeutics’ for the treatment of disease in humans.

Data availability statement

The datasets generated during the current study are available in the NCBI Sequence Read Archive (SRA). The RNA sequencing data is available under BioProject ID PRJNA894183 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA894183) and the Tn-seq data is available under BioProject ID PRJNA894187 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA894187). Additional data that support the findings of this study are available from the corresponding author [B.B.F.] upon reasonable request.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2023.2190303.

Additional information

Funding

This work was supported by grants from the Canadian Institutes of Health Research (MOP-136976; FDN-159935) to B.B.F.