European abalone (Haliotis tuberculata Linnaeus, 1758), marine herbivorous gastropods, were bred at the sea-based abalone farm France Haliotis, on the coast of Brittany, France (48°36′46 N; 4°33′30 W). In summer 2010, juveniles were bred on land in nursery tanks for a year before being transferred to sea-based experimental cages and fed with a mixed algal diet composed of P. palmata, S. latissima, and L. digitata for about 6 months. Abalone were then not fed for a week before the beginning of the experiment (Additional file 1: Figure S5). The experiment started in February 2012, and three abalone were randomly sampled from each cage. Abalone were then fed ad libitum every month with one of the monospecific diets: P. palmata, U. lactuca, L. digitata, S. latissima, and this was replicated in three cages for each algal treatment. About every 2 months from February 2012 to January 2013, 3 abalone were taken randomly from each of the 12 cages and the resulting 216 abalone were frozen at − 80 °C until further analysis of the digestive bacterial microbiota (Additional file 1: Figure S6). On the same dates, additional abalone were sampled for measurements of growth and sexual maturation and the fresh algal diet was sampled before abalone feeding to subsequently analyze algal biochemical composition (see Additional file 8 for details).