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Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea.

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PubMed ID: 30355801

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Battaglioli EJ, Hale VL, Chen J, Jeraldo P, Ruiz-Mojica C, Schmidt BA, Rekdal VM, Till LM, Huq L, Smits SA, Moor WJ, Jones-Hall Y, Smyrk T, Khanna S, Pardi DS, Grover M, Patel R, Chia N, Nelson H, Sonnenburg JL, Farrugia G, Kashyap PC

Sci Transl Med. Oct 2018

COMMENT: In this work the authors propose a new prophylactic dietary intervention for Clostridioides difficile infections (CDI) based on the proline auxothrophy that this opportunistic pathogen has. Using human fecal transplantation into germ-free mice they are able to see that the dysbiotic human gut microbiota of patients with diarrhea shows increased levels of free amino acids, especially proline and that it could be linked to the higher susceptibility to Clostridiodes difficile (formerly Clostridium difficile) infection. This is the design of the work that the authors did:

To evaluate community-specific effects on susceptibility to CDI, we modeled human gut microbial communities from representative healthy-like and dysbiotic patients in germ-free mice and challenged them with C. difficile. 

The microbiome analysis approach was the sequencing of 16S rRNA after 4 weeks of colonization in germ-free mice. After several transplant experiments they show that the Clostridiodes difficile loads in healthy-like mice were lower than those in dysbiotic mice at day 6. To characterize the phenotypes the authors did RNA-Seq on microbial mRNA extracted from the stool of dysbiotic and healthy-like mice. They also used targeted NMR to quantify amino acids in both groups, detecting that dysbiotic mice showed significantly increased concentrations of 12 amino acids, with proline showing the most significant difference. They also deteced that the expression of genes related with short-chain fatty acids (SCFAs) and secondary bile acids was reduced. These findings were confirmed using metabolomics.

Focused on proline the authors analyzed the expression of the gen prdA (D-proline reductase proprotein) essential for proline use. This was that they found:

Microbial RNA-seq gene expression profiles from dysbiotic and healthy-like mice revealed increased expression of prdA, one of the essential enzymatic components in Stickland fermentation,in healthy-like mice before C. difficile challenge. After C. difficile challenge, prdA expression was detected in both healthy-like and dysbiotic mice . However, in healthy-like mice, prdA expression was attributed to three commensal bacteria—Clostridium hylemonae, Dorea longicatena, and Lachnospiraceae bacterium 5_1_57FAA—whereas, in dysbiotic mice, prdA expression was exclusively attributed to C. difficile. This suggested that C. difficile was readily able to scavenge and use free proline in the dysbiotic gut microbiota.

To determine the importance of proline in the Clostridiodes difficile colonization they used a prdB mutant that is unable to use proline as an energy source and, as it was expect, saw that the mutants showed reduced colonization in dysbiotic mice.

All this work suggest that proline is an important factor in C. difficile colonization that could open some new intervention strategies. With that idea in mind the authors did experiments for analyzing the effect of proline availability and detected that dysbiotic mice with a proline-deficient diet had a fivefold decrease in C. difficile loads at day 1 after C. difficile challenge. To see the impact of other amino acids they also studied mice fed with a reduced protein diet detecting a 10-fold decrease in C. difficile load at day 1 after challenge.

This work provides a new strategy for prevention of Clostridiodes difficile infection:

Dietary proline is not essential for humans, and protein-based dietary interventions are partially protective in animal models of C. difficile infection, suggesting that a proline-deficient diet could be a simple actionable therapy for providing protection to at risk individuals

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Raquel Tobes