Project properties
Title Determining the functional redundancy of the pig gut pre- and post weaning
Group Systems and Synthetic Biology
Project type thesis
Credits 36
Supervisor(s) Mike Loomans, Jasper Koehorst
Examiner(s) Dr Jasper Koehorst; Dr Rob Smith
Contact info robert1.smith@wur.nl
Begin date 2025/01/28
End date
Description Piglets frequently suffer from diarrhea upon the abrupt switch from milk to solid feed, which is commonplace in the swine industry. The piglets experience stress and reduce their feed intake, impacting the gut microbiome and causing diarrhea in some cases. The current hypothesis states that functional redundancy in the pig gut makes the microbiome more resistant to these stress factors. We aim to apply a technique for determining functional redundancy in humans to pigs to confirm this [1]. As input, we plan to use a large amount of shotgun metagenomics data from piglets pre- and post-weaning, gaining a greater resolution than that has been seen in previous studies [2]. By combining novel techniques and a wealth of metagenomics data, we would like you to determine whether higher functional redundancy is indeed correlated with a more favourable outcome for pigs.

References related to project:
[1] Tian, L., Wang, X.-W., Wu, A.-K., Fan, Y., Friedman, J., Dahlin, A., Waldor, M. K., Weinstock, G. M., Weiss, S. T., & Liu, Y.-Y. (2020). Deciphering functional redundancy in the human microbiome. In Nature Communications (Vol. 11, Issue 1). Springer Science and Business Media LLC. https://doi.org/10.1038/s41467-020-19940-1

[2] Zemb, O., achard, caroline S., ESTELLE, J., cauquil, laurent, denis, catherine, billon, yvon, combes, sylvie, rogel-gaillard, claire, & gilbert, helene. (2024). Genetic selection for residual feed intake impacts the functional redundancy of the gut microbiota in pigs during the growing-finishing period. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.06.05.597549
Used skills
Requirements Basic knowledge of Python or R.