## 3 Results
### Microbial Community Composition  
The reciprocal Simpson diversity index is a measure of the diversity and evenness of the microbial community. When all donors were averaged, there was a significant increase in the reciprocal Simpson diversity index between the control and antibiotic periods in the PC lumen for both the untreated and treated chambers; the index returned to similar to, or significantly higher levels than control in the follow-up period (Table 1). In the DC lumen and the PC and DC mucus, the reciprocal Simpson diversity index was significantly decreased during the antibiotic period when compared to the control period for both untreated and treated. In the follow-up period, diversity returned to levels similar to, or significantly higher than the control period; there was no difference between untreated and treated. Thus, probiotics had no effect on the recovery of diversity following antibiotic treatment. Figure 1: Changes in acetate (**a**), propionate (**b**), butyrate (**c**), and lactate (**d**) over the control (\(n=12\)), antibiotic (\(n=12\); final timepoint), and follow-up (\(n=24\)) periods for pooled donors. Purple bars represent untreated chambers and green bars represent chambers treated with MegaSporeBioticTM. Levels in the AB and FU periods were compared to the control period and levels in the AB period were compared to the FU period using a two-tailed homoscedastic \(t\)-test; comparisons between the untreated versus treated groups were made using a two-tailed paired \(t\)-test. * indicates a significant (\(p<0.05\)) difference versus the control period, § indicates a significant (\(p<0.05\)) difference for the AB period versus the FU period, # indicates a significant (\(p<0.05\)) difference for untreated versus treated. AB, antibiotic period; C, control period; DC = distal colon; FU, follow-up period; PC = proximal colon. Antibiotic treatment resulted in changes at both the phylum level (Figure 2, Table S1 (individual donors, lumen), Table S2 (individual donors, mucus)) and family level (Figure 3, Table S3 (individual donors, lumen), Table S4 (individual donors, mucus)) as expected. Antibiotic treatment resulted in a significant decrease in all bacterial families in both the PC and DC of the lumen versus the control period (Figure 2a-e). In the mucus layer of the PC and DC, changes in the proportional abundance varied among phyla (Figure 2f). The abundance of _Bifidobacteriaceae_ changed notably with antibiotic treatment, accounting for the bulk of the changes in Actinobacteria levels (Figure 3b). In the follow-up period, the levels of Actinobacteria recovered and changes at the family level were similar for treated and untreated (Figure 3a). Overall, the results indicate a similar recovery in the untreated and treated arms. Bacteroidetes levels were significantly reduced in all colon regions in the antibiotic versus control periods (Figure 2a,b), which was mainly due to decreases in the following families: _Bacteroidaceae_ and _Tamerellaceae_ in all colon regions and _Rikenellaceae_ in the DC (Figure 3a,b). These levels recovered during the follow-up period and recovery was similar for the untreated and treated chambers. In the mucosal DC, the _Bacteroidaceae_ levels recovered to a higher extent in the treated arm (\(p<0.05\) versus the control period) than the untreated arm (Figure 3b). Firmicutes levels were significantly reduced between the control period and the antibiotic period in all colonic regions (Figure 2a,b), indicating a dysbiosised microbial community. This was mainly linked to a reduction in the butyrate-producing _Lachmospiraceae_, _Clostridiaceae_, and _Ruminococcaceae_ families, and the propionate-producing _Veillonellaceae_ family, and to a lesser extent, the lactate-producing _Enterococcaceae_ family (Figure 3a,b). Generally, Firmicutes levels recovered during the follow-up period and differences between the untreated and treated arms were limited (Figure 2).