## 3 Results
### Microbial Community Composition
_Bacillusae_ levels were significantly increased in the luminal PC and DC with treatment, which can be linked with the presence of bacterial species of this family in the MegaSporeBioticTM probiotic (Figure 3a). _Ruminococcaceae_ levels recovered to a significantly higher extent with treatment than without in both the luminal and mucosal PC; levels recovered to those observed in the control period with treatment but remained significantly decreased versus the control period without treatment (\(p<0.05\)) (Figure 3a,b). In the luminal DC the levels of _Clostridiaceae_ were significantly enhanced with treatment versus untreated and reached higher levels with treatment than were observed in the control period (Figure 3a). In the mucosal DC, a similar observation was made regarding the recovery of the butyrate-producing _Lachmospiraceae_ and the propionate-producing _Veillonellaceae_ families, and the opposite for unclassified Clostridia (Figure 3b). The Proteobacteria were increased with antibiotic treatment; increases were significant in most colon regions (Figure 2a,b) and were mainly linked with increases in _Enterobacteriaceae_, _Pseudomonadaceae_, and _Xanthomonadaceae_ (Figure 3a,b). Proteobacteria levels gradually decreased in the follow-up period, though they remained significantly elevated compared with the control period in all colonic regions (Figure 2a,b). There were limited differences between untreated and treated. _Enterobacteriaceae_ levels tended to decrease to a greater extent in the treatment arm versus untreated in the lumen (Figure 3a). \begin{table}
\begin{tabular}{l c c c c c c} \hline \hline  & \multicolumn{3}{c}{**Untreated**} & \multicolumn{3}{c}{**Treated**} \\ \cline{2-7}  & **Control** & **Antibiotic** & **Follow-Up** & **Control** & **Antibiotic** & **Follow-Up** \\  & **Period** & **Period** & **Period** & **Period** & **Period** & **Period** \\ \hline PC lumen & 6.06 & 9.62 * & 7.54 * & 5.87 & 8.28 * & 7.30 \\ DC lumen & 20.40 & 7.90 * & 22.64 * & 19.59 & 8.11 * & 23.66 * \\ PC mucus & 13.58 & 9.13 * & 10.97 & 11.34 & 8.41 * & 14.56 \\ DC mucus & 24.52 & 11.92 * & 23.27 & 24.31 & 11.77 * & 25.31 \\ \hline \hline \end{tabular} Data are presented as the average of donors A–D. * \(p<0.05\) versus control period.  
\end{table} 
Table 1: Average reciprocal Simpson diversity index. Figure 2: Average absolute abundance (cells/mL) of different phyla in the lumen. Actinobacteria (**a**), Bacteroidetes (**b**), Firmicutes (**c**), Proteobacteria (**d**), Verrucomicrobia (**e**), and average proportional abundance (%) of different phyla in the mucus (**f**) of the untreated and treated PC and DC compartment. The average values (\(n=12\)) of different phyla for data pooled from four different 6–24-month-old baby fecal donors (\(n=3\) for each donor). Samples were collected at the end of the control period, at the end of the antibiotic period, and at the end of the follow-up period. Dark blue bars represent Actinobacteria, orange bars represent Bacteroidetes, gray bars represent Firmicutes, yellow bars represent Proteobacteria, and light blue bars represent Verrucomicrobia. Levels in the antibiotic and follow-up periods were compared to the control period using a two-tailed homoscedastic \(t\)-test; comparisons between the untreated and 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 untreated versus treated. AB = antibiotic; C = control period; DC = distal colon; FU = follow-up period; PC = proximal colon. For _Akkermansia muciniphila_, the only representative of the Verrucomicrobia phylum, levels were significantly reduced after antibiotic treatment, most notably in the lumen (Figure 3a). While there was recovery of Verrucomicrobia abundance in the follow-up period, there were no differences between untreated and treated.