nd b](#f3){ref-type="fig"}). In the faecal pellets, the effects of PSG on the bacterial microbiome were the most heterogeneous, with a large number of high and significant effect sizes accompanied by relatively low PIPs ([Figure 3a](#f3){ref-type="fig"}). Unlike PSG, vancomycin was associated with a lower number of significant effects. However, these effects were more consistent. In the terminal ileum, PSG and vancomycin had a similar pattern of effects on the bacterial microbiome, and the signatures in the ileum were more consistent than those in the faecal pellets ([Figure 3b](#f3){ref-type="fig"}). In both GI sites, bacterial genera belonging to the *Bacteroidetes* and *Firmicutes* phyla had the most consistent antibiotic signatures with higher PIPs.

In the faecal pellets, PSG consistently and significantly suppressed most genera on both days 7 and 21 ([Figure 3c](#f3){ref-type="fig"}). Most of these genera were members of phyla *Bacteroidetes* and *Firmicutes*. By contrast, *Parabacteroides* was the only genus that increased in relative abundance in the PSG-treated mice on days 7 and 21. Even though vancomycin reduced the relative abundance of several of the same genera as did PSG, the magnitude of the reduction was smaller in comparison. In addition, vancomycin increased multiple genera, including *Lactobacillus*, *Proteus*, *Cronobacter*, *Anaeroplasma*, *Parasutterella* and *Mucispirillum*.

In the terminal ileum, PSG treatment had a mixed effect, decreasing the relative abundance of some genera, but increasing others ([Figure 3d](#f3){ref-type="fig"}). The increase in *Enterococcus*, *Streptophyta* and *Anaeroplasma* was especially notable at day 21 in the presence of *C. albicans* colonization. Vancomycin also had a similar mixed effect. It depleted the same genera as did PSG, including "*Candidatus Arthromitus*" which is known to stimulate a Th17 response in the GI tract[@b15][@b16]. However, vancomycin treatment increased a greater number of genera than did PSG, especially on day 7.

On day 7, the fun