## 4 Discussion  
The effect of daily supplementation of MegaSporeBiotic(tm) spore-based probiotic formulation on the recovery of the microbial community activity and microbial community composition after antibiotic-induced dysbiosis was assessed using a Baby-Quad-M-SHIME(r) model evaluating the microbiota from four individual baby donors. Recovery with probiotic treatment was compared to that of untreated (i.e., spontaneous recovery). SCFA levels decreased significantly from the control period upon antibiotic treatment and recovered similarly in both the untreated and treated groups. In the follow-up period, levels of acetate and propionate had recovered to levels similar to the control period for most donors while levels of butyrate were increased over the antibiotic period but remained significantly lower than in the control period, indicating that a longer recovery time was necessary. The recovery of lactate levels in the PC varied somewhat between donors, making the results difficult to interpret, but there were no major differences in recovery for untreated versus treated. In the DC, lactate levels were very low in the control period and increased significantly in the antibiotic period. Given that lactate is a substrate for SCFA production [32; 33; 34; 35] and the fact that SCFA production was significantly decreased during the antibiotic period, this may indicate a loss of lactate-utilizing bacteria after antibiotic treatment, as lactate accumulation is associated with dysbiosis [36; 37; 38]. Lactate levels were reduced in the follow-up period, potentially reflecting the observed microbiota recovery. Overall, our findings showed a similar recovery of microbial metabolic activity with or without treatment with MegaSporeBiotic(tm), suggesting that probiotic intervention did not aid in recovery from antibiotic-induced dysbiosis in the Baby-SHIME(r) model. Treatment appeared safe in that there were neither increases in microbial pathogens nor signals of dysbiosis with treatment. These findings are important given that there is a paucity of data for the use of probiotics in infants following antibiotic treatment. Regarding the microbial community composition, antibiotic treatment reduced the abundance of Actinobacteria, Bacteroidetes, Firmicutes, and Verrucomicrobia and increased the levels of Proteobacteria, indicating a dysbiosised microbial community. When antibiotics were stopped, a consistent spontaneous recovery of the microbial community composition was observed for all four donors. There were minimal differences between untreated and treated, indicating an overall similar microbial recovery for both test conditions. Robotic supplementation to infants throughout the first 6 months of life revealed minimal changes in the infant gut microbiome, with the only difference from untreated being an increase in the abundance of _Bifidobacterium_ in the first week of treatment [39]. Therefore, it may not be surprising that probiotic supplementation had little effect on the infant gut microbiome. However, it must be noted that the participants in that study were administered a variety of probiotics (parent's choice), so the findings are very generalized and do not relate to specific probiotic strains. There is also some evidence that breastfeeding versus formula feeding affects the response of the infant microbiome to probiotic treatment. A strong impact on the gut microbiota composition was observed for infants who received antibiotics and probiotics and were breastfed while the same was not true for those who were formula fed [40]. The feed used in our study was based on formula feed rather than breastmilk, which may have affected our results. It is of interest to evaluate whether probiotic strains engraft with treatment. We observed a significant increase in the _Bacillusae_ family during the follow-up period in both the PC and DC of the treated chambers, indicating that there was at least partial engraftment of the probiotic strains.