Edited by Margaret McFall-Ngai, University of Hawaii at Manoa, Honolulu, HI, and approved March 13, 2021 (received for review October 30, 2020)Microbes have a strong impact on the biology of their host, with those living in the gut being essential to immunity, development, and metabolism. A functional gut, however, has been lost several times during animal evolution. Here, using sister sea urchin species, we report that the loss of a functional gut corresponds with a reduced microbial diversity and abundance. Gut loss also coincides with associating with an endosymbiont that complements...…Edited by Margaret McFall-Ngai, University of Hawaii at Manoa, Honolulu, HI, and approved March 13, 2021 (received for review October 30, 2020)Microbes have a strong impact on the biology of their host, with those living in the gut being essential to immunity, development, and metabolism. A functional gut, however, has been lost several times during animal evolution. Here, using sister sea urchin species, we report that the loss of a functional gut corresponds with a reduced microbial diversity and abundance. Gut loss also coincides with associating with an endosymbiont that complements...WW…