Gut protist diversity in Eurasian beavers (Castor fiber) revealed by metabarcoding

Gut protists are an important part of the microbial community that is often overlooked or limited to certain "flagship" species, mainly parasites. This also applies to Eurasian beavers (Castor fiber), which act as aquatic engineers in riparian habitats and have been identified as potential reservoirs of the well-known intestinal protist parasite - Giardia intestinalis. In this study, we focus on exploring protistan diversity in Eurasian beavers from freshly collected stool samples using molecular methods, including targeted barcoding of specific parasitic groups (Giardia, Cryptosporidium and Microsporidia) and general metabarcoding of the V4 region of 18S rRNA on the Illumina MiSeq platform. Two individuals were tested positive for Cryptosporidium spp. using the targeted barcoding. The metabarcoding approach revealed that the gut community was predominantly composed of gut commensals, Blastocystis, and trichomonads, found in every individual. More detailed investigation of Blastocystis confirmed the potential existence of a specific beaver subtype. Colpodellids and parasitic Eimeria spp. were only occasionally present. Geographic location of the host, unlike sex, has a significant impact on gut microbiota composition, though more research is needed due to limited sampling. Finally, we tested a new primer set for amplifying the V4 region of 18S rRNA, which shows promise for improving the detection of Metamonada protists in the gut samples.