The longitudinal effect of a multi‐strain probiotic on the intestinal bacterial microbiota of neonatal foals

REASONS FOR PERFORMING THE STUDY: The microbiota plays a key role in health and disease. Probiotics are a potential way to therapeutically modify the intestinal microbiota and prevent disease. OBJECTIVES: The aim of this study was to investigate the effects of probiotics on the bacterial microbiota of foals during and after administration. STUDY DESIGN: Randomised placebo controlled field trial. METHODS: Thirty‐eight healthy neonatal foals enrolled in a previous study were selected. The foals had received a multi‐strain probiotic (four Lactobacillus spp. 3–4 × 10³ colony‐forming units (cfu)/g each, Bifidobacterium animalis spp. lactis, 1 × 10³–⁴ cfu/g) or placebo once daily for 3 weeks. A total of 3 faecal samples were collected from each foal at 2‐week intervals and assessed via metagenomic sequencing. The Wilcoxon test was used to compare data between treatment groups. RESULTS: There were no changes on the phylum, order or class level between treatment groups at any age (all P>0.05) but some significant changes in relative abundance of families. Probiotic administration did not result in an increased relative abundance of lactobacilli or bifidobacteria at any age (Lactobacillus: P = 0.9, P = 0.1 and P = 0.2, Bifidobacterium: P = 0.3, P = 0.6 and P = 0.1 for Weeks 2, 4 and 6, respectively). Lactobacillus was enriched in the probiotic group at Week 6 on LEfSe analysis (linear discriminant analysis score 0.34, P = 0 .02). There was no effect on alpha diversity (all P>0.2) or community structure when parsimony and unifrac analysis were applied (all P>0.6). CONCLUSIONS: There were limited effects of probiotic treatment on the bacterial microbiota of foals. The studied probiotic based on lactobacilli and bifidobacteria has a limited potential for therapeutic modification of the gastrointestinal microbiota.