As it is closely surrounded by the gonads, the digestive gland could not be separated from the gonads during dissection. The gonado-digestive gland (simplified as the digestive gland throughout the manuscript) of 216 abalone was thus dissected as a whole and was freeze-dried before tissue grinding (Additional file 1: Figure S7). DNA was extracted from ground lyophilized glands and the V3-V4 variable region of the 16S rRNA gene was amplified using primers targeting Bacteria. Amplicons from three abalone of the same conditions (same cage and same sampling date) were then pooled before MiSeq paired-end sequencing (Illumina, San Diego, CA, USA), which resulted in about 10 million sequence reads. Sequence quality check, curation, alignment, and chimera removal were done using publicly available scripts (fastx_toolkit, http://hannonlab.cshl.edu/fastx_toolkit/; get_paired.py, http://abims.sb-roscoff.fr, mothur v.1.34.4, ). Sequences were taxonomically classified with the RDP classifier  on the Silva release 119  and OTUs were clustered at 97% sequence identity using the average neighbor algorithm (see Additional file 8 for details, ).