| Summary: | (1) Background: <i>Blastocystis</i> is a microbial eukaryote inhabiting the gastrointestinal tract of a broad range of animals including humans. Several studies have shown that the organism is associated with specific microbial profiles and bacterial taxa that have been deemed beneficial to intestinal and overall health. Nonetheless, these studies are focused almost exclusively on humans, while there is no similar information on other animals. (2) Methods: Using a combination of conventional PCR, cloning and sequencing, we investigated presence of <i>Blastocystis</i> along with <i>Giardia</i> and <i>Cryptosporidium</i> in 16 captive water voles sampled twice from a wildlife park. We also characterised their bacterial gut communities. (3) Results: Overall, alpha and beta diversities between water voles with and without <i>Blastocystis</i> did not differ significantly. Differences were noted only on individual taxa with <i>Treponema</i> and <i>Kineothrix</i> being significantly reduced in <i>Blastocystis</i> positive water voles. Grouping according to antiprotozoal treatment and presence of other protists did not reveal any differences in the bacterial community composition either. (4) Conclusion: Unlike human investigations, <i>Blastocystis</i> does not seem to be associated with specific gut microbial profiles in water voles.
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