A lovely story, well written, starting with keen observation, pursued logically and exciting in its implications.  If it is found, as surmised, that nasal carriage of SA is secondary to gut carriage, that would indeed be important.  Alternatively, it is may be that the bacillus inhibitors of AIP can reach the nares from the gut and inhibit colonization there also.

Perhaps, in any cultivated site, the microbial population of native plants (''weeds") , competitors which are usually targeted by herbicides, are an important resource for the desired crop.  If so, an appropriate distribution of a herbicide-resistant weed species might improve crop yield.