At the later stage of infection, if insects are still living, the detoxification system activated under Bt spores, Cry toxins, and their combined doses, mostly mitigate the toxicosis at 48 h.p.i. Interestingly, Bt spores and/or Cry toxins do not alter the midgut bacterial composition much after 48 h in living insects, but those that die at the same time-point do show altered abundances of various genera and clear evidence of Bt replication—presumably in preparation of sporulation. This evidence concerns the gene CRYL1 and infection.