Grey and harbor seals in France (mainland and Saint-Pierre et Miquelon): microbial communities and identification of a microbial source tracking seal marker

The bacterial communities of grey and harbor seals were not found to be significantly different and were characterized by a predominance of Firmicutes, including the genera <i>Clostridium sensu stricto</i> 1 and <i>Peptoclostridium</i>, followed by Fusobacteriota with the genus <i>Fusobacterium</i>, and Bacteroidota with the genus <i>Bacteroides</i>. However, variations in bacterial communities between sites and individuals were observed. Similar observations were made for the RNA viral communities being characterized by a predominance of <i>Picobirnaviridae</i> (44% of total reads) and <i>Astroviridae</i> (15%). This study successfully developed a sensitive (89.8%) and specific (97.1%) MST qPCR marker targeting grey seal-associated bacteria belonging to the Bifidobacteriaceae family. This marker can be used to identify potential fecal contamination of coastal areas by seals and complements the MST toolboxes of markers already developed for humans, wild birds and livestock.