Study of the microbiota associated to Ruditapes decussatus and Ruditapes philippinarum clams by 16S rRNA metabarcoding, dilution to extinction, and culture-based techniques

The study of the microbiota associated to clams is important not only to know their sanitary status but also to prevent pathobiology events. The use of different microbiological techniques can help to obtain a better picture of the bacterial diversity of clams as well as to isolate new bacterial taxa. In this study, two clam species, Ruditapes decussatus and R. philippinarum, were analyzed in two locations of Galicia (northwest of Spain) in April and October, by combining classic culturing, dilution-to-extinction approach, and 16S rRNA gene target sequencing. 16S rRNA gene target sequencing revealed a great diversity within the clam samples, shedding light into the vast microbial communities associated to these bivalves. All samples were dominated by the same bacterial genera in the different periods, namely Mycoplasma, Vibrio, and Cutibacterium. The alpha-diversity in the samples obtained during the month of October was lower and showed the dominance of rare bacterial taxa, such as Methylobacterium or Psychrobacter. Dilution-to-extinction technique demonstrated its usefulness to culture rare bacterial taxa that were not found in clams under the classic culturing techniques, including Rahnella, Brachybacterium, Micrococcus, Jantinobacter, and Lelliottia. Altogether, our study provides valuable information on the microbiota associated to R. decussatus and R. philippinarum, demonstrating the high complexity and dynamics of these microbial populations.