An integrated multi-omics protocol for swine feces reveals congruent longitudinal dynamics in microbiome structure and function

Today, the pig is regarded as promising biomedical model, however, its gastrointestinal microbiome dynamics have been less investigated than that of humans or murine models. The aim of this study was to establish a high-throughput multi-omics pipeline to investigate the healthy fecal microbiome of swine and its temporal dynamics as basis for future infection studies. To this end, a preparation and analyses protocol based on deep-frozen feces including integrated sample preparation for different meta-omics analyses was developed. Subsequent data integration linked microbiome composition with function and metabolic activity with protein inventories, i.e. 16S rRNA data and expressed proteins, and identified proteins with secreted metabolites. 16S rRNA gene amplicon and metaproteomics analyses revealed a fecal microbiome dominated by Prevotellaceae, Lactobacillaceae, Lachnospiraceae, Veillonellaceae, Ruminococcaceae and Clostridiaceae. Similar microbiome composition in feces and colon, but not ileum samples, was observed, showing that feces can serve as minimal-invasive proxy for porcine colon microbiomes. Longitudinal dynamics in composition, e.g. increased abundance of Lactobacillaceae and Streptococcaceae during the experiment, were not mirrored in microbiome functioning. Instead, metaproteomics and metabolomics showed a rather stable functional state, as evident from SCFA profiles and associated metaproteome functions, pointing towards functional redundancy among microbiome members. In conclusion, our multi-omics pipeline generates highly reproducible data on the intestinal microbiota taxonomy and functionality of swine.