Our experiment was carried out in an abalone farm located at the French Brittany coast where waters are impacted by seasonal variations specific to this permanently mixed ecosystem [69, 70]. These temperate coastal waters were coldest in February–April 2012 and January 2013 (10–11.5 °C) and warmest from June to October 2012 (12.5–15 °C, Additional file 6: Table S5). Several studies in temperate coastal areas showed seasonal succession and structuring of the bacterial community [39, 41, 71]. Accordingly, even if three genera were dominating for the entire year, the community structure of abalone digestive microbiota was impacted by seasonal variability (Fig. 1), and 17.6% of the biological variation of the microbiota was explained by the effect of sampling dates alone and by its combined effect with abalone characteristics and algal biochemical content. We found one study on seasonality of intestinal microbiota in a marine organism, the farmed Atlantic salmon, which showed highest number of bacteria in the gut with the highest temperature in August but a community composition that was quite stable over the year . More temporal studies were done in fresh water, where several examples of seasonality of fishes’ digestive microbiota could be observed either in terms of cell number or taxonomic composition . In our study, however, the biochemistry of the four algae showed significant seasonal variations through the year, as tested with their content in soluble carbohydrates, dry algal matter and protein (Friedman test with post hoc test after Nemenyi, Roussel, personal communication), which had a significant effect on the digestive microbiota, explaining 5.4% of the biological variation of the microbiota (Additional file 1: Figure S4). Also, individual microbial genera of the dominant core and the less abundant microbiota were differently correlated with temporal fluctuations of contextual parameters (Fig. 5). For instance, the presence of Vibrio, Psychromonas, an unclassified Rhodobacteraceae, Polaribacter, and Pseudahrensia was positively correlated with increasing water temperature (Fig. 5). Seasonal variations have been previously described for Vibrio and Polaribacter in the plankton and in particle-attached fractions in coastal waters [41, 74], but no study could be found on seasonality in coastal waters of Psychromonas and of Pseudahrensia. Seasonal fluctuations of Vibrio and the less abundant and diet-specific core microbiota may thus be not only influenced by algal diet biochemical content but also by the seasonality of the water column composition.