As an employee of the agricultural biotechnology sector, I can attest that the industry takes any new studies related to the safety of GM crops very seriously. As such, I reviewed the paper by Carman et al. with interest at the time it was published and reread in order to best answer your question. The paper reports that pigs fed GMOs had inflamed stomachs based on visual evaluation of redness. However, the paper also shows that pigs fed non-GMO diets also had inflamed stomachs. The authors chose not to comment on the table in the paper that shows there were more pigs with inflamed stomachs that had eaten the non-GMO diet than the GMO diet. Stomach inflammation is common in animals with high feed intake or feed that has been finely ground. The feed intake is not reported in this paper. Without additional information about the study (beyond that reported in the paper), other, non-feed-related factors could account for the observed results.
Swine in the United States have been consuming GM grains for more than 15 years; this includes the breeding herd. According to USDA, the reproductive performance of the breeding herd has improved steadily over that period. With missing details and selected results analyzed in the Carman et al. paper, the paper lacks credibility in opposition to the hundreds of food and feed safety studies conducted on GMOs and the 15 years of practical experience. DuPont Pioneer has directly investigated GM and non-GM grain in livestock diets as well, and we have not detected any health or performance differences. See here for an example of one such study, or check out the Biofortified website, where independent experts are reviewing the science of plant genetics and working on a list of the more than 600 studies related to the safety of GM crops.
The Food and Drug Administration (FDA) and other regulatory authorities worldwide conduct their own peer reviews on the science provided by biotech product developers. Additionally, as scientists, FDA reviewers also review the published literature. This process helps ensure the safety of food from GM plants.