Publishing
In the Pipeline
Here is what I'm working on these days. Papers in this section are rotating through various stages of preparation and submission
Pepin, D. M.*, Burckhardt, J. C.*, He, J., McCallum, G., Ng, K., Trotter, V., Van Treuren, W., Sonnenburg, J.L, Deutschbauer, A., & Tropini, C. Engineering gut bacteria depleted by industrialization to survive malabsorption.
Pepin, D. M., Popple, S., Srinivas, A., He, J., Sie, C., McCallum, G., Ng, K., Ghezzi, H., Vallance, B., Osborne, L., & Tropini, C. The loss of Muribaculaceae, a vanishing family of gut commensal bacteria, results in long-term changes to intestinal physiology.
Pepin, D. M., Forgie, A. J., Munyaka, P. M., Fouhse, J. M., Ju, T., Kommadath, A., Yadav, P., Stothard, P., & Willing, B. (In preparation). Re used litter increases intestinal microbial diversity reducing Salmonella enterica colonization in young broiler chicks.
Dissertations
Doctor of Philosophy, UBC with Dr. Carolina Tropini
Functional impact of osmotic perturbation on the gut microbiota.
Characterized the impact of osmotic stress on the gut microbiota and the loss of bacterial family Muribaculaceae, a vanishing family of gut commensal bacteria.
Master of Science, U of A with Dr. Benjamin Willing
The microbial modifying properties of re-used chicken litter and iodinated water on poultry health and disease resistance.
Investigated the effects of iodinated water and chicken litter exposure on early establishment of intestinal microbiota, resistance, growth performance, and host intestinal transcriptome in poultry.
Publications
Ghezzi, H., Fan, Y.M., Ng, K.M., Burckhardt, J.C., Pepin, D. M., Lin, X., Ziels, R.M. and Tropini, C. (2024). PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification. Msphere, 9(7), pp.e00360-24.
Ng, K. M.*, Pannu, S.*, Liu, S., Burckhardt, J. C., Hughes, T., Van Treuren, W., Nguyen, J., Naqvi, K., Nguyen, B., Clayton, C. A., Pepin, D. M., Collins, S. R., & Tropini, C. (2023). Single-strain behavior predicts responses to environmental pH and osmolality in the gut microbiota. Mbio, e00753-23.
Ju, T., Bourrie, B. C., Forgie, A. J., Pepin, D. M., Tollenaar, S., Sergi, C. M., & Willing, B. P. (2023). The Gut Commensal Escherichia coli Aggravates High-Fat-Diet-Induced Obesity and Insulin Resistance in Mice. Applied and Environmental Microbiology, 89(3), e01628-22.
Forgie, A. J., Pepin, D. M., Ju, T., Tollenaar, S., Sergi, C. M., Gruenheid, S., & Willing, B. P. (2023). Over supplementation with vitamin B12 alters microbe-host interactions in the gut leading to accelerated Citrobacter rodentium colonization and pathogenesis in mice. Microbiome, 11(1), 1-22.
Nguyen, J., Pepin, D. M., & Tropini, C. (2021). Cause or effect? The spatial organization of pathogens and the gut microbiota in disease. Microbes and Infection, 23(6-7), 104815.
Forgie, A.J., Gao, Y., Ju, T., Pepin, D.M., Yang, K., Gänzle, M.G., Ozga, J.A., Chan, C.B. and Willing, B.P. (2019). Pea polyphenolics and hydrolysis processing alter microbial community structure and early pathogen colonization in mice. The Journal of Nutritional Biochemistry, 67, 101-110.
*Willing, B. P., Pepin, D. M., Marcolla, C. S., Forgie, A. J., Diether, N. E.,&Bourrie, B. C. (2018). Bacterial resistance to antibiotic alternatives: a wolf in sheep’s clothing?. Animal Frontiers, 8(2), 39-47. (*All authors are co-first authors).
Kalan, L. R., Pepin, D. M., Ul-Haq, I., Miller, S. B., Hay, M. E., & Precht, R. J. (2017). Targeting biofilms of multidrug-resistant bacteria with silver oxynitrate. International Journal of Antimicrobial Agents, 49(6), 719-726.
Clayton, C., McCallum, G., Ng, K., Srinivas, A., Sie, C., Tertigas, D., Porter, I., Pepin, D. M., Fardeen, T., Sinha, S., and Tropini, C. (In submission). Bowel preparation-induced changes in the gut environment facilitate pathogen and pathobiont colonization.