The Guardian ran an article a while back talking about GM gene's jumping to bacteria in an eater's intestine. Has other research confirmed this phenomenon?
There is nothing special about a piece of GM DNA when compared to any other random piece of DNA. If this phenomenon happened at any detectable level, we'd have found eukaryotic DNA in bacterial genomes/plasmids long before the introduction of genetically modified crops. And that would be front page news in the field of horizontal gene transfer! Which has many talented people in it!
Of far greater concern is the transfer of genetic material between bacteria in which antibiotic resistance is conferred. The firmicutes in your poop is not at all the same genetically speaking as the firmicutes in my poop. Polymorphisms and genetic transfer have changed members of the gut microbiome and that leads to differential extraction of energy from the ingested food and differential behavior with respect to antibiotics.
Apparently transfer between prokaryote and eukaryote (in both directions) has been detected: http://www.biomedcentral.com/1471-2148/11/276/abstract http://www.sciencedirect.com/science/article/pii/S0888754311001959 http://genome.cshlp.org/content/19/8/1441.abstract
Some numbers I'd like to know are the rate of pro<->eu HGT detection /versus the rate of looking for it/ (i.e. 3 confirmations in 300 attempts would be more impressive than 3 confirmations in 30,000 attempts).