A metaproteomic analysis of the piglet fecal microbiome during the weaning transition

Authors: Rivera-Colon, Israel; HARKOW, KALYNN - US Department Of Agriculture (USDA); COLE, ROBERT - Johns Hopkins University School Of Medicine; O'MEALLY, ROBERT - Johns Hopkins University School Of Medicine; Garrett, Wesley; XIONG, WEILLI - Food And Drug Administration(FDA); Oliver, William; Wells, James; Summers, Katie; CHHETRI, NISAN - North Carolina State University; Postnikova, Olga; Rempel, Lea; Crouse, Matthew; Neville, Bryan; Davies, Cary

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/3/2024
Publication Date: 4/29/2025
Citation: Rivera-Colon, I., Harkow, K., Cole, R., O'Meally, R., Garrett, W.M., Xiong, W., Oliver, W.T., Wells, J., Summers, K.L., Chhetri, N., Postnikova, O.A., Rempel, L.A., Crouse, M.S., Neville, B.W., Davies, C.L. 2025. A metaproteomic analysis of the piglet fecal microbiome during the weaning transition. Frontiers in Microbiology. 16. Article e1504433. https://doi.org/10.3389/fmicb.2025.1504433.
DOI: https://doi.org/10.3389/fmicb.2025.1504433

Interpretive Summary: The breakdown and absorption of carbohydrates, alongside the production of short-chain fatty acids plays an indispensable role in the growth, immunity and intestinal development of pigs. The gut microbiota contributes to the breakdown and absorption of all macronutrients but play a critical role in the metabolism of carbohydrates and the production of short-chain fatty acids. Therefore, disruptions the microbial community can affect digestibility and growth performance. Due to dietary and physiological changes, microbial dysbiosis is common at weaning and alterations to the gut microbiota often result in lifelong growth impairment in young pigs. Traditionally, in-feed antibiotics were used to ease the weaning transition, but with current limitations on antibiotic usage, novel therapeutics are needed. Despite growing knowledge of the critical role of microbes in post-wean digestion and health, many mechanisms by which microbes contribute to piglet well-being remain unclear. Here, we used a quantitative metaproteomics approach to characterize global microbial protein abundance in the piglet gut before and after weaning and highlight carbohydrate digestive processes. We determine which microbiome taxa are responsible for carbohydrate degradation and SCFA synthesis. In pre-wean piglets, proteins critical for SCFA generation corresponded to taxa commonly associated with the breakdown of milk-specific carbohydrates, whereas the proteome of post-wean piglets contained a greater abundance of similar proteins that were from taxa capable of breaking down plant-specific carbohydrates. Furthermore, output revealed that production of propionate takes place via the propionaldehyde pathway in pre-wean piglets, but changes to production via the succinate pathway in post-wean piglets. Finally, a disproportionate amount of carbohydrate-active enzyme (CAZyme) activity (~8%) was due to the activity of fungi, which typically only represent ~1% of the microbiome taxa. Together, this information will facilitate the design of novel therapeutics which target the gut microbiome during the weaning transition to improve piglet health and performance.

Technical Abstract: Microbiome analysis has relied largely on metagenomics to characterize microbial populations and subsequently predict their functional roles. Here, we used a metaproteomic analysis of the fecal microbiome in piglets before and after weaning to compare protein abundance and expression as they pertain to microbial populations specific to either a milk- or plant-based diet. Fecal samples were collected from six piglets on the day of weaning and four weeks after transitioning to a standard nursery diet. Using the 12,554 protein groups identified in samples, we confirmed the shift in protein composition that takes place in response to the microbial succession following weaning and demonstrated the redundancy in metabolic processes between taxa. We identified taxa with greater roles as primary degraders based on corresponding proteins synthesized, thereby providing evidence for cross-feeding. In pre-wean piglets, proteins critical for SCFA generation corresponded to taxa commonly associated with the breakdown of milk-specific carbohydrates, whereas the proteome of post-wean piglets contained a greater abundance of similar proteins that were from taxa capable of breaking down plant-specific carbohydrates. Furthermore, output revealed that production of propionate takes place via the propionaldehyde pathway in pre-wean piglets, but changes to production via the succinate pathway in post-wean piglets. Finally, a disproportionate amount of carbohydrate-active enzyme (CAZyme) activity (~8%) was due to the activity of fungi, which typically only represent ~1% of the microbiome taxa. Information gathered through this characterization of the proteome before and after weaning revealed important differences regarding the role of members in the microbial community, thereby providing information for the optimization of diets and products for both piglet and microbiome health.