I believe that Dr. Falkinham addressed this concern. He explained that the water first goes through the 0.2 micron filter and then passes through the lower carbon filter. Therefore, the NTM is filtered out of the water before it reaches the carbon filter. You should feel safe when using the Lifestraw pitcher, but you do still need to disassemble it periodically and thoroughly clean inside, placing the filters to the side while you do this. I usually place mine on paper towels, add Dawn to the main pitcher reservoir along with very hot water (tap), thoroughly wash, then rinse and dry with paper towels.

I believe that, realistically, we will never be free of any and all bacteria in our environment, but the goal is to reduce exposure as much as possible.