It is a well-established principal of toxicology that often "the dose makes the poison." When an organic farmer sprays Bt bacteria on food crops, the bacteria produce the Bt toxin. The amount of the Bt toxin present is incredibly small, it is only on the surface of the plant, and it degrades in the presence of sunlight and water in about a day. It is doubtful that anyone eating organic food sprayed with this bacteria would have detectable levels of the toxin this bacteria produces in their blood.
Now compare how organic farmers use Bt to what happens with GMO Insecticidal corn. With GM corn, the gene from the Bt bacteria that enables the bacteria to produce the toxin, has been inserted into the corn plant in such a manner that now every cell in the entire corn plant is continuously producing that toxin in amounts large enough to kill any caterpillar who attempts to eat any part of the plant. This means the toxin is now present in amounts many orders of magnitude higher than ever before, and being produced within the cells little if any would be degraded by sunlight and rain. This is why we can now find this toxin in the bloodstream of pregnant women and in the cord blood of their babies.
While some have speculated that the Bt toxin might also cause holes in the human gut, as it does in the insect gut, leading to leaky gut syndrome, allergies and more, I am not aware of any published studies that confirm this. However a lot of insecticidal GMO corn, is also specifically engineered to be resistant to the herbicide glyphosate (Round-up). This enables farmers who grow it to spray extremely large amounts of Round-up on the corn fields to kill all the weeds -- and not have it damage the corn crop. While Monsanto argues that GM crops can reduce the use of herbicides, the fact is, Round-up sales and use has skyrocketed because of this technology, and likely anyone consuming GMO corn has also increased their exposure to Round-up. Now we have evidence that Round-up itself may be a factor contributing to leaky gut in humans.
Furthermore, I think there is an even bigger hypothetical risk --based upon one of my daughter's high school science fair projects (for which she was given an award by the EPA.) My daughter was looking to see if antibiotic resistance could be passed from genetically modified corn to gut bacteria (a gene for antibiotic resistance is typically inserted in the corn gene as part of the GMO process). Although she was not able to demonstrate such a transfer, her experiment did reveal a surprising phenomenon: The longer GMO corn plants decomposed. the less likely e coli bacteria (a normal inhabitant of a healthy gut) were to live and grow at all after exposure to the remains of the corn. Her data raised the possibility that eating GMO's could dramatically alter the gut microbiome -- which a growing body of research makes clear could have profound impacts on gut health, immune system functioning, general levels of inflammation in our bodies and even how our brain works and how likely we are to suffer with depression!