A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function.

Area of Science:

• Microbiology
• Animal Science
• Biomedical Research

Background:

• Swine are valuable biomedical models, yet their gastrointestinal microbiome dynamics are understudied compared to humans and mice.
• Understanding the swine microbiome is crucial for advancing its use in biomedical research.

Purpose of the Study:

• To establish an integrated multi-omics protocol for investigating the fecal microbiome of healthy swine.
• To link microbiome composition with function and metabolic activity.

Main Methods:

• Developed a comprehensive sample preparation and analysis protocol for deep-frozen swine feces.
• Utilized 16S rRNA gene amplicon sequencing and metaproteomics for microbiome analysis.
• Integrated data to correlate microbiome composition, protein expression, and metabolite profiles.

Main Results:

• The fecal microbiome was dominated by Prevotellaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae, and Clostridiaceae.
• Fecal microbiome composition mirrors the colon but not the ileum, validating feces as a non-invasive proxy.
• Microbiome function, indicated by short-chain fatty acid profiles and metaproteomics, remained stable despite temporal compositional shifts, suggesting functional redundancy.

Conclusions:

• The developed multi-omics pipeline provides congruent data on swine intestinal microbiome taxonomy and functionality.
• Feces can serve as a reliable proxy for the porcine colon microbiome.
• Swine gut microbiome exhibits functional stability and redundancy, even with dynamic taxonomic shifts.