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Background  Natural populations inhabiting the rocky intertidal experience multiple ecological stressors and provide an opportunity to investigate how environmental differences influence microbiomes over small geographical scales. However, very few microbiome studies focus on animals that inhabit the intertidal. In this study, we investigate the microbiome of the intertidal barnacle  Semibalanus balanoides . We first describe the microbiome of two body tissues: the feeding appendages, or cirri, and the gut. Next, we examine whether there are differences between the microbiome of each body tissue of barnacles collected from the thermally extreme microhabitats of the rocky shores’ upper and lower tidal zones.    Results  Overall, the microbiome of  S. balanoides  consisted of 18 phyla from 408 genera. Our results showed that although cirri and gut microbiomes shared a portion of their amplicon sequence variants (ASVs), the microbiome of each body tissue was distinct. Over 80% of the ASVs found in the cirri were also found in the gut, and 44% of the ASVs found in the gut were also found in the cirri. Notably, the gut microbiome was not a subset of the cirri microbiome. Additionally, we identified that the cirri microbiome was responsive to microhabitat differences.    Conclusion  Results from this study indicate that  S. balanoides  maintains distinct microbiomes in its cirri and gut tissues, and that the gut microbiome is more stable than the cirri microbiome between the extremes of the intertidal.    Supplementary Information  The online version contains supplementary material available at 10.1186/s42523-020-00058-0.

Characterizing the cirri and gut microbiomes of the intertidal barnacle Semibalanus balanoides