Microbiome Profile of the Mediterranean Mussel (Mytilus galloprovincialis) from Northern Aegean Sea (Greece) Culture Areas, Based on a 16S rRNA Next Generation Sequencing Approach

Mediterranean mussels (Mytilus galloprovincialis), due to their nutritional mechanisms which involve filtering huge amounts of water, are affected by seawater pollution and can host microbial diversity of environmental origin, as well as pathogenic bacteria that must be constantly monitored. Herein, we applied a Next Generation Sequencing (NGS) metabarcoding approach in order to study the M. galloprovincialis microbiota. Collection of samples was conducted during winter and summer months from various mussel farm zones located in specific farm regions in the Thermaikos gulf, the northern Aegean Sea, Greece. A microbiological test was performed for the enumeration of Escherichia coli and the presence of Salmonella sp. DNA extraction and amplification of the whole bacterial 16S rRNA gene, followed by NGS amplicon sequencing and taxonomic classification, were carried out. Statistically significant differences (p < 0.05) in the abundance of the most dominant bacterial phyla, families and genera between winter and summer time periods, regions, as well as zones within each region of sampling, were evaluated with z-score computation. According to the obtained results, the most prevalent taxa at the genus level were Mycoplasma (12.2%), Anaplasma (5.8%), Ruegeria (5.2%) and Mariniblastus (2.1%). Significant differences in the abundance of the most dominant genera were found at all levels of comparison (seasons, regions and zones within each region), highlighting the dynamic character of microorganisms, which might be affected by microenvironmental, temporal and spatial changes. The present research contributes to the characterization of M. galloprovincialis microbiome in areas that have not been studied previously, setting the baseline for future, more thorough investigations of the specific bivalve species and its bacterial profile in the above geographic regions.