Fig. 3

Next-generation sequencing of the 16S rRNA gene amplicon from caecal fluid. a Untargeted principal component analysis of log-ratio transformed OTU abundance by sample, showing closer clustering associated with shipment batch than with treatment class. b, c Alpha diversity, measured by the inverse Simpson index (40.7 vs 58.5, p = 0.043 by Student’s t test with Welch’s correction, b) and Shannon index (4.53 vs 4.81, p = 0.046, c). d Relative abundances of major phyla in each sample, grouped by batch and treatment group. There were no significant differences when analysed by batch or by treatment groups. e Taxonomic attributions of OTUs differentially abundant when analysed by shipment batch and treatment class, assessed using the Analysis of Composition of Microbiomes (ANCOM) framework with alpha set at 0.05 and a cutoff value of 0.6