The suppression of coral recovery by macroalgae, called as coral-macroalgal shift, is an increasing phenomenon in coral reefs worldwide. Such ecosystem change is known to impact reef microbial communities but few studies have examined the effect on animal microbiota. Fishes play an important ecological role in coral reef ecosystems and represent an important source of proteins for local populations. Modification of their microbiota through exposure to allochthonous bacteria orchange in the availability or quality of their food resource could alter these ecosystems services. In order to understand the consequence of coral macroalgal shift on coral fish microbiota, we examined the response of 99 fish gut bacteriomes belonging to 36 species as well as macroalgae bacteriomes in 7 reefs of the Inner Seychelles islands. Fish gut bacteriomes differed strongly from macroalgae bacteriomes. The latter were highly influenced by the environmental conditions between island, sites, substrate and regime of the reef. In contrast, the coral macroalgal shift did not influence the diversity, composition, or variability of fish gut bacteriomes which were markedly determined by the taxonomy and the diet with carnivorous and herbivorous clearly distinct. Macroalgal bacteriome seemed to influence the variability of their consumers with a significant response to the site on the variability of the core enteric microbiome of Siganidae. The distribution of their host was clearly impacted depending on its diet preferences with a substitution of the Scaridae by the Siganidae in macroalgal invaded sites. These families was marked by different bacterial classes but did not differed in the functions cared by their bacteriomes thanks to the functional redundancy. These results suggested that, even the enteric microbiomes of reef fish are relatively resistant across perturbated sites and do not alter the fitness of their hosts with potential consequences on the ecosystem services, the contribution of the microbial functions would be shifted or eroded with the host distribution.
