We, or at least I, was misinterpreting this study.
Although it's still an abstract it will be published and my friend contacted the person and explained it.
Here is a longer part of his priliminary study:
http://www.paratuberculosis.info/web/images/proc11/379.pdf
^^ this study in fuller makes much more sense than the link on top to understand what he actually means
Checking for MAP antigen DNA doesn't mean you get just results from live MAP, it could very well be dead MAP (he refers to it as "
heat killed MAP", from the pasteurisation process)
He is talking about MAP antigen, which doesn't have to be live MAP at all, it will still evoke an immune response. Live MAP doesn't explain the reaction of IL-10 they see, in animals live MAP increases IL-10 and IL-10 is needed to have a correct immune response, it decreases inflammation, but dead MAP can explain this.
So even boiling the milk wouldn't work, you would still get
dead MAP and invoke a response. (that warning from Pfizer about the suspended MAP in oil from their vaccine causing a granuloma reaction when mistakingly self-injected was with dead MAP too, there is no live MAP in that vaccine)
The reason he said "reconsider 'MAP infection'" is because he doesn't see the same response in Ptb from a live infection, he thinks it's the result of MAP antigen from killed MAP from pasteurisation for example (pasteurisation doesn't kill all MAP but it can partially kill MAP)
I think this paper is really important even though I have a hard time understanding it and it is still "in process", which means the full will be released in a couple of weeks hopefully.
NOD2 is also involved in autophagy, which is partly responsible for clearing 'debris' from pathogens.
(I hope this is correctly interpreted now, it's confusing to me until he explained it)
He says to avoid all dairy too, because it doesn't matter if you kill the MAP with boiling it or not, it's going to evoke an antigen immune response.