3.3 | Genetic stability of a model mixed bacterial community in culture
To assess the genetic stability of the bacterial community in long-term culture, the bioreactors were connected in series to create a dynamic model of the human digestive tract. In this experiment, six bioreactor modules were connected in series, each set to maintain a specific pH and held under anaerobic conditions to simulate a segment of the human gastrointestinal tract (Figure 4A). The pH values used in the stomach, small intestine, and large intestine compartments were based on the pH values reported for these regions of the human digestive tract (Khutoryanskiy, 2015). At the start of the experiment, Module 1 (representing the stomach) was inoculated with the model microbiota as described earlier (Figure 4B) and the system was operated continuously for 120 h. As shown in Figure 4C-4H, bacterial density in Module 1 decreased (Figure 4C), while the bacterial density in Modules 2 and 3 (representing the proximal and distal small intestine, respectively; Figures 4D and 4E) as well as Modules 4-6 (representing the ascending colon, transverse colon and descending colon of the large intestine, respectively; Figures 4F-4H) increased over the duration of the experiment. Modules 4-6 exhibited the greatest bacterial density. At the end of the experiment, the genetic composition of the bacterial community in Module 6, which simulates the most distal large intestine compartment (Figure 4H), closely resembled that of the initial inoculum (Figure 4B) at the genus level. The specific bacterial species and their abundance in each of the bioreactor modules in the series were also determined. The composition of the bacterial community was distinct at different pH represented by the different segments of the digestive tract (Figure 4A). B. bifidum was not detectable after 24 h of culture, suggesting that specific nutritional or structural substrate requirements of this particular species that may have not been met by the culture conditions. In contrast, L. casei ,L. rhamnosus , B. longum , and S. thermophilus remained easily detectable throughout the entire duration of the experiment (Figure S3).