Propagules of most animals and plants encounter a resource-limited situation after dispersal. Alates of termites definitely face such a situation, which found a new colony by a monogamous pair without any help from workers. How do they manage limited resources including nutrition reserves and gut microbes for wood digestion during colony foundation? To reveal this, we analyzed time-series data of reproduction schedules, gut microbial fluctuations, and resource allocation patterns in the founders of incipient termite colonies of a subterranean termite, Reticulitermes speratus. We found “gut microbial pulse”, i.e., steep increase and rapid decrease of the amounts of intestinal protozoa that occurred at the timing of larval hatching. Our data suggest that resources derived from the pulse play an essential role in parental provisioning to larvae. The present study highlights a novel strategy that termites use to overcome resource-limited situations and successfully establish a new colony.