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Metabolic adaption to extracellular pyruvate triggers biofilm formation in Clostridioides difficile

Abstract

Clostridioides difficile infections are associated with gut microbiome dysbiosis and are the leading cause of hospital-acquired diarrhoea. The infectious process is strongly influenced by the microbiota and successful infection relies on the absence of specific microbiota-produced metabolites. Deoxycholate and short-chain fatty acids are microbiota-produced metabolites that limit the growth of C. difficile and protect the host against this infection. In a previous study, we showed that deoxycholate causes C. difficile to form strongly adherent biofilms after 48 h. Here, our objectives were to identify and characterize key molecules and events required for biofilm formation in the presence of deoxycholate. We applied time-course transcriptomics and genetics to identify sigma factors, metabolic processes and type IV pili that drive biofilm formation. These analyses revealed that extracellular pyruvate induces biofilm formation in the presence of deoxycholate. In the absence of deoxycholate, pyruvate supplementation was sufficient to induce biofilm formation in a process that was dependent on pyruvate uptake by the membrane protein CstA. In the context of the human gut, microbiota-generated pyruvate is a metabolite that limits pathogen colonization. Taken together our results suggest that pyruvate-induced biofilm formation might act as a key process driving C. difficile persistence in the gut.

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Fig. 1: The T4aP machinery is required for biofilm formation in BHISG supplement with DOCA.
Fig. 2: Overview of transcriptomic changes over time in genes previously associated with stationary phase in C. difficile strain 630Δerm grown in BHISG supplemented with 240 µM DOCA.
Fig. 3: Biofilm formation in BHISG supplement with DOCA is dependent on SigH, SigL and PTS transport.
Fig. 4: Combination of branched-chain amino acid, cysteine and mucus-derived sugars induce biofilm formation in BM supplemented with 240 µM DOCA.
Fig. 5: Presence of extracellular pyruvate induces biofilm formation.
Fig. 6: Biofilm formation in the presence of pyruvate is CtsA dependent.
Fig. 7: Proposed model of cellular processes leading to DOCA-induced biofilm formation.

Data availability

RNA-Seq data generated in this study are available in the NCBI-GEO with accession no GSE165116.

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Acknowledgements

We would like to thank Johann Peltier, Imane El Meouche and Laurent Bouillaut for generously providing the CDIP634, fliC::erm, rex::erm and prdB::erm strains. This work was funded by the Institut Pasteur and the “Integrative Biology of Emerging Infectious Diseases” (LabEX IBEID) funded in the framework of the French Government’s “Programme Investissements d’Avenir”. YDNT postdoctoral fellowship was funded by the LabEX IBEID.

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Tremblay, Y.D.N., Durand, B.A.R., Hamiot, A. et al. Metabolic adaption to extracellular pyruvate triggers biofilm formation in Clostridioides difficile. ISME J (2021). https://doi.org/10.1038/s41396-021-01042-5

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