# A metaproteomic analysis of the piglet fecal microbiome across the weaning transition

## TL;DR

This study uses metaproteomics to analyze how the piglet gut microbiome changes in protein activity before and after weaning, revealing shifts in diet-related functions and microbial roles.

## Contribution

The study provides novel insights into microbial protein activity shifts during weaning, highlighting cross-feeding and diet-specific metabolic adaptations.

## Key findings

- Proteins related to milk carbohydrate breakdown dominate pre-weaning, while plant carbohydrate-degrading proteins increase post-weaning.
- Fungi contribute disproportionately to carbohydrate-active enzymes despite being a small fraction of the microbiome.
- Propionate production shifts from the propionaldehyde pathway in pre-weaned piglets to the succinate pathway post-weaning.

## Abstract

Microbiome analysis has relied largely on metagenomics to characterize microbial populations and predict their functions. Here, we used a metaproteomic analysis of the fecal microbiome in piglets before and after weaning to compare protein abundances 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 4 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 roles as primary degraders based on corresponding proteins synthesized, thereby providing evidence for cross-feeding. Proteins associated with the breakdown of milk-specific carbohydrates were common among pre-weaned pigs, whereas the proteome of post-weaned piglets contained a greater abundance of proteins involved in the breaking down plant-specific carbohydrates. Furthermore, output revealed that production of propionate takes place via the propionaldehyde pathway in pre-weaned piglets, but changes to production via the succinate pathway in post-weaned piglets. Finally, a disproportionate quantity of carbohydrate-active enzymes (CAZymes) (~8%) were produced by fungi, which typically only represent ~0.1% of the microbiome taxa. Information gathered through this characterization of the metaproteome 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.