To investigate the dynamics of the oyster microbiota (Crassostrea gigas) in two oyster families after exposure to the infectious environment (Brest, France, July 2015), we analyzed total bacterial communities using 16S metabarcoding during the first 72h in mesocosm experiment. We have analyzed a total of 42 samples which represents two oyster families at 7 kinetic times (0, 6, 12, 24, 48, 60, 72 hours post infection) in triplicates (three groups of ten oysters). For each sample, 16S rDNA amplicon libraries were generated using the 341F (5’-yanCCTACGGGNGGCWGCAG-3’) and 805R (5’-GACTACHVGGGTATCTAATCC-3’) primers targeting the variable V3V4 loops for bacterial communities. Paired-end sequencing with 250 bp read length was performed at the McGill University (Génome Québec Innovation Centre, Montréal, Canada) on the MiSeq system (Illumina) using the v2 chemistry according to the manufacturer’s protocol. A total of 4.692.744 sequence reads were obtained from 42 libraries. After cleaning steps, 2.475.189 sequences corresponding to 8.428 OTU were kept for further analyses. In addition, the overall transcriptomic responses of oysters families were studied by RNA-seq over the time-course of the mesocosm experiment. In total, the sequencing of 42 samples (2 families, 7 time points, in triplicates) yielded between 20.4 and 32.3 millions of Illumina paired reads per sample: from 69.7% to 75.3% of the reads mapped to the C. gigas V9 reference genome. RNA-seq results were validated by qPCR on 30 genes at all sampling times in both oyster families (r² = 0.936).