Q: Do you think after some time Donor A in Study 3 will have its bacterial ecosystem return back to its original pre-infection state?
A: The salmonella infection caused certain niches to be wiped out from the bacterial ecosystem of Donor A which were then filled in by similar type of bacteria and reached to a different ecosystem at a new equilibrium. Since these niches are dominated by the new groups of bacteria, it would not be possible for the previous bacterial groups to replace them without a large-scale change in his gut ecosystem.
Q: Is the death of certain bacterial groups in the gut during salmonella infection caused directly by the infection or is it an immune response to cure the disease?
A: It can be both, but it is very hard to tell from the data in Study 3 since it is only a data point that corresponds to the event that we can observe. A future study that tries to figure out what is happening in our immune system during the infection can be observed by drawing blood from the patients during the infection.
Q: Is there a particular connection between an individual’s genome and the dominant bacterial groups in the bacterial ecosystem? Would twins show more similar bacterial ecosystems?
A: Twins in general have similar bacterial ecosystems independent from whether they live together or are separated. Even though this seems to be a genetic factor at first, monozygotic and dizygotic twins have the exact same effect, as well as displaying similarity to their mothers’ bacterial ecosystem. The reason for this is that starting from birth there is a period of time in which the bacterial ecosystem is programmed. The similarity effect between twins is based on this more than genetic factors.