Sadly, TENS output was intentionally made different so that it would not be very effective in killing microbes.
If the zapper that you use is killing something in your gut, then that is good but it is obviously not doing the complete job. In fact, holding it directly over the gut is probably short circuiting much of the signal. Electricity takes the shortest path ( path of least resistance ) which in the case of your unit, 90 percent of the electricity goes straight from one tiny contact to the other tiny contact.