The impact of fructooligosaccharide supplementation on the gastrointestinal microbiome of Thoroughbred youngstock during nutritional stress

Background: Feeding of domesticated horses with carbohydrate-rich diets is associated with a high risk of gastrointestinal (GI) diseases. Prebiotic supplements, such as fructooligosaccharides (FOS), are promoted as 'gut stabilizers' by reducing potentially pathogenic bacteria in the GI tract in response to carbohydrate overload. However, studies supporting FOS use have had mixed results and use outdated culture-based techniques.Objectives: To evaluate the impact of FOS prebiotics on the GI microbiome of Thoroughbred yearlings by genetic profiling of the microbiome. Study Design: Randomized case-control study.Methods: 12 male Thoroughbred yearlings were recruited by random selection into 2 groups: a prebiotic group (receiving 30g/day FOS dietary supplement for 8 weeks) and a control group (no FOS supplement). Samples were taken prior to supplementation and subsequently bi-weekly and were analyzed through microbial 16S rRNA sequencing. Qiime 2 and Calypso were used for bioinformatics and statistical analysis.Results: The prebiotic and control group had statistically significant differences in microbiome composition and diversity in the baseline sample prior to prebiotic administration. There were no significant global GI microbiome changes over time following FOS supplementation compared to the control group. Some saccharolytic bacterial species showed diverging (increasing in FOS and decreasing in control) patterns of abundance over time between groups.Main Limitations: The small sample number may reduce the relevance of the results. Also, additional factors, such as social interactions and individual wellbeing, could influence the GI microbiome.Conclusions: Contrary to previous culture-based studies, this preliminary study shows limited effects of FOS administration on the GI microbiome, however, the alterations in abundance of some saccharolytic bacterial species show potential for further investigation. Furthermore, the difference in baseline microbiomes between our study groups prior to FOS supplementation highlight the importance of baseline samples in interventional microbiome research.