Chitosan is an antimicrobial chemical that can be inexpensively synthesized from chitin, a waste product of the shrimp industry. Forest Products Laboratory scientists are now trying to determine if this naturally derived chemical can be used to protect mass timber from termite damage in green building construction. Research showed that, at high enough concentrations, chitosan caused 100% mortality of subterranean termites. The mechanism appeared to involve changes in diversity of the microbes living in the termite hindgut. These microscopic organisms, which are primarily composed of protists and bacteria, are essential to termite survival because they break cellulose down into compounds that can be absorbed and used by the termite for growth. We found that termites fed sub-lethal amounts of chitosan exhibited a 12-fold reduction in total protist counts with only 2 of 10 protist species surviving compared to controls. Moreover, significant changes in bacterial diversity included establishment of three different species of bacterial pathogens. Although it is impossible to know what and how a termite feels, the observed microbial imbalance induced by the chitosan could very well be giving termites the worst “stomach ache” imaginable.