## 4 Discussion
### Shifts Observed in the Bacterial Community Composition following Inoculation  
Once the fermenters were inoculated, the evolution of target taxa was assessed by qPCR analyses of the fermentation samples. The qPCR method is a convenient and reproducible technique that allows for mapping of the distribution of phylogenetically distinct bacteria with high sensitivity [40]. Thus, a relative profile of fifteen microbial communities in the batch fermentation was drafted, as presented in Figure 2a-o. In general, the microbial richness seemed to be affected upon inoculation. Similar effects have been observed in previous studies and underlined the need for control experiments to study the induced effects of different treatments due to the very probable loss of taxa during the experiment setup and simulated fermentation [65]. However, this is not the case here, since only untreated microbiota were analyzed. A diminution was observed during the colon experiment for the Firmicutes phylum (the most abundant phylum in the inoculum), as shown in Figure 2b. However, a lactic acid-producing bacteria (LAB) belonging to this phylum (the _Enterococcus_ genus) had an exponential increase during the 72 h fermentation (Figure 2l). This important colonization of _Enterococcus_ was very consistent in the three replicated colonic systems. Some strains belonging to the _Enterococcus_ genus are considered negative biomarkers of gut health due to their association with inflammatory bowel disease (IBD) [74] and with outbreaks of nosocomial infections [75]. However, several strains from this genus are health promoters [76]. For example, they are recommended in the treatment of serum cholesterol (_E. facecium_ M-74) [77], antibiotic-associated diarrhea (_E. facecium_ SF68) [78], and irritable bowel syndrome (_E. facecalis_ DSM 16440) [79]. Moreover, a very recent study of the newly isolated _Enterococcus lactis_ strain JDM1 assessed its probiotic potential and good gastrointestinal tolerance [80]. Other LAB genera quantified in the colon microbiota (_Lactobacillus_ and _Streptococcus_), behaved very differently from _Enterococcus_. On the one hand, _Lactobacillus_ (Figure 2l) seemed to increase during only the first day of the colon simulation. On the other hand, _Streptococcus_ presented a high increase in the microbiota for two days, and then significantlydecreased by the third day (Figure 2m). The presence of the _Lactobacillus_ genus in human colonic microbiota has been either positively or negatively related to health [81]. Some strains such as _L. reuteri_ can greatly contribute to metabolizing tryptophan into indole derivatives, and thereby activate the AhR in the host's epithelial barrier, as well as limit the colonization of opportunistic pathogens [82]. Meanwhile, members of the _Streptococcus_ genus are anciently known to cause life-threatening infections. However, recent studies have suggested the potential probiotic uses of some species such as _S. salivarius_[83] and _S. thermophilus_[84]. Together, the previous observations relative to LAB growth tendency could indicate a significant change in the incubated ecosystem by the third day of static fermentation. This might be caused by the production of toxic metabolites and could justify limiting the batch culture to 48 h, as others have suggested [71; 72; 85]. Nevertheless, the significant increase observed in the _Bifidobacterium_ genus (Figure 2j) and in _Bacteroides-Prevotella_ (Figure 2n) advocates in favor of a longer (72-h) fermentation. Such increases were not significant, but very consistent at the phylum level. On the one hand, the Actinobacteria phylum had a relatively constant profile during the incubation, which increased on the third day, as the _Bifidobacterium_ genus. Various members of Bifidobacterium are among the earliest colonizers of the human gastrointestinal tract [86], and the genus is the subject of increasing interest as a health promoter [87; 88].