Diverse but desolate landscape of gut microbial azoreductases: A rationale for idiopathic IBD drug response

ABSTRACT

Prodrugs reliant on microbial activation are widely used but exhibit a range of efficacies that remain poorly understood. The anti-inflammatory compound 5-aminosalicylic acid (5-ASA), which is packaged in a variety of azo-linked prodrugs provided to most Ulcerative Colitis (UC) patients, shows confounding inter-individual variabilities in response. Such prodrugs must be activated by azo-bond reduction to form 5-ASA, a process that has been attributed to both enzymatic and non-enzymatic catalysis. Gut microbial azoreductases (AzoRs) are the first catalysts shown to activate azo-linked drugs and to metabolize toxic azo-chemicals. Here, we chart the scope of the structural and functional diversity of AzoRs in health and in patients with the inflammatory bowel diseases (IBDs) UC and Crohn’s Disease (CD). Using structural metagenomics, we define the landscape of gut microbial AzoRs in 413 healthy donor and 1059 IBD patient fecal samples. Firmicutes encode a significantly higher number of unique AzoRs compared to other phyla. However, structural and biochemical analyses of distinct AzoRs from the human microbiome reveal significant differences between prevalent orthologs in the processing of toxic azo-dyes, and their generally poor activation of IBD prodrugs. Furthermore, while individuals with IBD show higher abundances of AzoR-encoding gut microbial taxa than healthy controls, the overall abundance of AzoR-encoding microbes is markedly low in both disease and health. Together, these results establish that gut microbial AzoRs are functionally diverse but sparse in both health and disease, factors that may contribute to non-optimal processing of azo-linked prodrugs and idiopathic IBD drug responses.

KEYWORDS:

• Azoreductase
• microbial metabolism
• Irritable Bowel Disease
• Sulfasalazine
• Structural Metagenomics
• Multi-omics
• metagenomics
• Structural Biology

Acknowledgments

We like to thank current and previous Redinbo lab members for helpful discussions. Figure 1a,b were created with BioRender.com. We would also like to acknowledge that a manuscript analyzing AzoR enzymes was published while this manuscript was under review, titled “Gut microbiome-wide search for bacterial azoreductases reveals potentially uncharacterized azoreductases encoded in the human gut microbiome” DOI: 10.1124/DMD.122.000898.

Disclosure statement

M.R.R. is a founder of Symberix, Inc., which is developing microbiome-targeted therapeutics. M.R.R. also receives research funding from Merck and Eli Lilly.

Author contributions

J.B.S., B.S.C., and M.R.R. conceptualization; J.B.S., B.S.C, and J.J.S. data curation; J.B.S. formal analysis; J.B.S., B.S.C., and J.J.S. investigation; J.B.S., B.S.C. and M.R.R. writing – original draft; J.B.S., B.S.C., J.J.S. and M.R.R. writing – review and editing; J.B.S. and M.R.R. supervision; J.B.S., B.S.C., and J.J.S. methodology; J.B.S. and M.R.R. funding acquisition; M.R.R. project administration.

Data availability statement

The datasets supporting the conclusions of this article are included within the article and its additional files.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2023.2203963

Additional information

Funding

This work was supported by NIH grants GM137286 and GM135218 (M.R.R.) and by NSF DGE-1650116 (J.B.S).