Machine learning models reveal Saccharomyces yeasts are associated with poor piglet growth in early development

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.