Over a year, 10–15% OTUs were shared by the 4 monospecific diets. For all sampling dates pooled per algal diet, 22% of the OTUs of the whole community corresponded to a core community shared by the 4 diets (Fig. 3). To better understand the potential functioning of this core community, we focused on temporal fluctuations of these OTUs constantly found in the digestive microbiota. We considered as the core microbiota only the OTUs occurring in all samples, considering each of the four algal diets, for each cage triplicate and during the whole year. Six OTUs belonging to the classes Fusobacteriia, Gammaproteobacteria, and Mollicutes fit this definition: one Psychrilyobacter OTU, two Vibrio OTUs, two Mycoplasma OTUs, and an unclassified OTU. In terms of sequence read abundance, these six OTUs represented about 86% of the microbiota (Fig. 4), although relative contribution of each of these OTUs was variable (Fig. 2). Apart from these 3 dominating core genera, 5 to 8 additional genera belonged to a core microbiota specific to each algal diet and they represented lower relative abundances of OTUs, ranging from 0.001 to 24.5% of sequence reads per cage (Fig. 4). Some OTUs belonged to genera found with at least two monospecific diets: Lutimonas, Psychromonas, Roseobacter, and four unclassified genera. Other genera were specific to a given diet. Polaribacter and Pseudahrensia were associated with the P. palmata diet, Escherichia-Shigella to the U. lactuca diet, Roseibacillus to the L. digitata diet, and Ulvibacter was associated with the S. latissima diet (Fig. 4).Fig. 3Comparison of the microbial OTU composition associated with the four algal diets. Comparisons are described by proportions of shared or unique OTUs and were made for each sampling date from February 2012 to January 2013 and for the six sampling dates pooled according to diet. D, L. digitata; S, S. latissima; P, P. palmata; U, U. lactucaFig. 4Composition of the digestive core microbiota at the genus level associated with a monospecific diet. Pie charts on the left represent proportions of sequence read abundances, at the genus level, representative of the core microbiota of a monospecific diet. Pie charts on the right represent detailed proportions of less abundant genera representative of the core microbiota of a monospecific diet