Fig 3.

Amoxicillin treatment influenced gut-associated microbial composition, as displayed by distinct clustering in the principal coordinates plot of Bray Curtis dissimilarity on day 21 (A). Each dot represents fecal microbiota of one piglet (Anosim P = 0.01). Alpha diversity was no longer distinct in piglets treated with amoxicillin on day 21 as indicated by Chao1 and Shannon index (P = 0.453 and P = 0.562, respectively, B). Stacked bar chart displays predominating phyla, calculated as a percentage of total 16S rRNA reads (C). Taxonomic differences between amoxicillin and placebo-treated piglets were identified by DeSEq2. Taxa enriched in amoxicillin are shown in blue; taxa enriched in placebo piglets are shown in green (D). (*P < 0.05; #P ≤ 0.10).