@article{rivera_harlow_cole_robert_garrett_xiong_oliver_wells_summers_chhetri_et al._2025, title={A metaproteomic analysis of the piglet fecal microbiome across the weaning transition}, DOI={10.3389/fmicb.2025.1504433}, abstractNote={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.}, journal={Frontiers in Microbiology}, author={Rivera, Israel and Harlow, KaLynn and Cole, Robert N. and Robert, O’Meally and Garrett, Wesley and Xiong, Weili and Oliver, William and Wells, James E. and Summers, Katie Lynn and Chhetri, Nisan and et al.}, year={2025}, month={May} }
 @article{chhetri_summers_campos_postnikova_rivera_harlow_oliver_wells_davies_2025, title={Machine learning models reveal <i>Saccharomyces</i> yeasts are associated with poor piglet growth in early development}, DOI={10.1093/jas/skaf133}, abstractNote={Abstract Modern swine production relies on consistent growth rates across individuals to maximize efficiency and earnings, but a subset of piglets are born small and grow slowly. Nutrition and management practices can augment the growth of slow growers but there remains a substantial portion of piglets that never reach their full growth potential. Traditionally, in-feed antibiotics were administered to enhance growth but with limitations on use, alternatives are needed. Emerging evidence suggests a role for bacterial members of the gut microbiome in growth, but fungal members have been largely overlooked. Yeasts have been used in the swine industry to improve health and growth, but a limited number of species have been utilized, and study results are mixed. Here, we use ITS2 sequencing to profile the mycobiome of piglets at 2 timepoints in early development, postnatal days 14 (D14) and 21 (D21), just before weaning. Pigs were classified as either good or poor growers, with pigs below the 40th percentile of average daily gain labeled as poor growers, while those above the 60th percentile were labeled as good growers. A total of 27 samples from good growers were analyzed from D14 (n = 27), 27 from poor growers at D14 (n = 27), 29 from good growers at D21 (n = 29), and 28 from poor growers at D21 (n = 28). Machine learning algorithms and differential abundance analyses were applied to identify fungi associated with both growth categories. At D14, Saccharomycetes yeasts are moderately predictive of poor growth, with the yeast genera Pichia, Lodderomyces, Clavispora, more abundant in poor growers than in good growers. Wallemia is significantly more abundant in good growers than in poor growers at D21. Additional fungi were associated with good and poor growth but data were sparse and further large-scale studies are needed to verify these observations. Together, these results contribute to our understanding of the role of the mycobiome in piglet growth and suggest that the reduction of yeasts in early development may improve performance across the weaning transition and beyond.}, journal={Journal of Animal Science}, author={Chhetri, Nisan and Summers, Katie Lynn and Campos, Philip and Postnikova, Olga and Rivera, Israel and Harlow, Kalynn and Oliver, William T and Wells, James E and Davies, Cary Pirone}, year={2025}, month={Jan} }