Background:Faecalibacterium prausnitzii, one of the most important bacteria of the human gut microbiota, produces butyrate (a short-chain fatty acid). Short-chain fatty acids are known to influence thyroid physiology and thyroid cancer’s response to treatment. We aimed to analyze the relative abundance ofFaecalibacterium prausnitziion the gut microbiota of differentiated thyroid cancer patients compared to controls and its variation after radioiodine therapy (RAIT). Methods: Fecal samples were collected from 37 patients diagnosed with differentiated thyroid cancer before and after radioiodine therapy and from 10 volunteers. The abundance ofF. prausnitziiwas determined using shotgun metagenomics. Results: Our study found that the relative abundance ofF. prausnitziiis significantly reduced in thyroid cancer patients compared to volunteers. We also found that there was a mixed response to RAIT, with an increase in the relative and absolute abundances of this bacterium in most patients. Conclusions: Our study confirms that thyroid cancer patients present a dysbiotic gut microbiota, with a reduction inF. prausnitzii’srelative abundance. In our study, radioiodine did not negatively affectF. prausnitzii, quite the opposite, suggesting that this bacterium might play a role in resolving radiation aggression issues.