Development of A Rational Framework For Understanding The Efficacy of Fecal Microbiota Transplantation In Calf Diarrhea Prevention

Abstract Background: Establishing fecal microbiota transplantation (FMT) to prevent multifactorial diarrhea in calves is challenging because of differences in farm management practices, the lack of optimal donors, and recipient selection. In this study, the underlying factors of successful and unsuccessful FMT trials are elucidated, and the potential markers for predicting successful FMT are identified using fetal metagenomics via 16S rRNA gene sequencing, fecal metabolomics via CE-TOFMS, and machine-learning approaches. Results: 20 FMT trials, in which feces from healthy donors were intrarectally transferred into recipient diarrheal calves, were conducted with a success rate of 70%. Selenomonas was identified as a microorganism genus that showed significant donor–recipient compatibility in successful trials. A strong positive correlation between the microbiome and metabolome data, which is a prerequisite factor for FMT success, was confirmed by Procrustes analysis in successful trials (r = 0.7439, P = 0.0001). Additionally, weighted correlation network analysis confirmed the positively or negatively correlated pairs of bacterial taxa (family Veillonellaceae) and metabolomic features (i.e., amino acids and short chain fatty acids) responsible for FMT success. Further analysis aimed at establishing criteria for donor selection identified the genus Sporobacter as a potential biomarker in successful donor selection. Low levels of metabolites, such as glycerol 3-phosphate, dihydroxyacetone phosphate, and isoamylamine, in the donor or recipients prior to FMT are predicted to facilitate FMT. Conclusions: Overall, we provide the first substantial evidence of the factors related to FMT success or failure; these findings could improve the design of future microbial therapeutics for preventing diarrhea in calves.