Microbiome Taxa Involved in Carbohydrate Breakdown and Synthesis of Short Chain Fatty Acids in the Piglet Gut

Abstract The gut microbiome plays a critical role in swine health and growth, and diet is a key factor which shapes microbiome communities. In particular, the fermentation of indigestible carbohydrates by microbes has important consequences for microbiome composition and host health. Pigs do not encode all the enzymes needed to breakdown dietary polysaccharides, but bacteria contain numerous carbohydrate-active enzymes (CAZys) which contribute to this task. In addition, microbial fermentation of carbohydrates produces many bioactive metabolites such as short chain fatty acids (SCFAs). The relationships between microbes, dietary components, and the pig are complex, but a thorough understanding of these interactions would promote the design of interventions which target the microbiome and improve swine growth, especially during the critical weaning transition. At weaning, the microbiome undergoes rapid compositional changes as the diet shifts from milk to plant based. Here, we use quantitative (TMT)-based liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify and quantitate piglet and microbial proteins in the gut during the weaning transition, with a focus on those involved in carbohydrate breakdown and nutrient synthesis. We analyzed 6 fecal samples from healthy, nursery piglets at weaning [day 21 postnatal (PN)] and 6 samples taken two weeks later, after acclimation to nursery diet (day 49 PN). In total, we detected 14,319 bacterial and fungal protein groups and 1,835 pig protein groups, and abundances of roughly one-half of the protein groups changed significantly over time (P = 0.05, fold change > 1.5). As expected, from weaning to day 49 PN, expression of glycoside hydrolases (GHs) which degrade milk oligosaccharides decreased, while the abundance of most enzymes which degrade plant carbohydrates such as xylan, cellulose, and starch, increased. Some plant-degrading enzymes were most abundant during weaning, which may reflect the tendency for piglets to steal solid feed from their mothers during nursing. Subdoligranulum was one of the top producers of multiple GHs capable of degrading milk or plant carbohydrates, while other genera specialized in the production of enzymes which targeted either milk oligosaccharides (Blautia, Lachnoclostridium Clostridium, Fournierella, Faecalibacterium, Eisenbergiella) or plant carbohydrates (Prevotella, Selemonas, Anaerovibrio). Aspergillus produced an uncharacterized protein predicted to degrade plant xyloglucan, highlighting the contributions of fungi in swine digestion. Host glycan-degrading enzymes decreased over time. Last, we detected acetate and butyrate production enzymes including acetate kinase (26 genera) and phosphate acetyltransferase (9 genera), and butyrate kinase and phosphate butyryltransferase from Subdoligranulum. Together, these data identify specific enzymes and the microbes that produce them during the transition from a milk to plant-based diet. This information provides a more robust understanding of digestion in the weanling pig and will ultimately provide a basis for effective design of probiotics and other therapeutics which target the gut microbiome to enhance swine growth and productivity.