And I was looking for the answer on whether FMTs are a guarantor for clearance of fungal abundance in the small intestinal or colonic lumen.
Surprisingly, it's a no!
It appears to be even the other way round.
Here's something interesting IMO about FMTs:
Gut fungal dysbiosis correlates with reduced efficacy of fecal microbiota transplantation in Clostridium difficile infection, 2018
In this study, it is shown that CDI is strongly accompanied by over-representation of Candida albicans and decreased fungal diversity, richness, and evenness.
Post-FMT, successful responders lack their previous C. albicans dominance but rather display a high relative abundance of Saccharomyces and Aspergillus.
High abundance of C. albicans in donor stool also correlates with reduced FMT efficacy.
In essence, therefore, annihilation of Candida dominance in CDI patients is crucial for FMT success and arguable it could be much advisable to pre-/co-treat any CDI with antifungals along with either ABx or FMT.
Another study showed contrasting results of FMT on UC:
Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis, 2020
Herein they showed that in contrast to FMT in CDI, clinically successful response to FMT in UC very much depended on high Candida abundance at baseline, which decreased after FMT. The authors argue that the prior Candida dominance may provide a specific niche for bacterial engraftment, ameliorating UC.
So, the very opposite of the pre-conditions in CDI.
However, what the authors do not talk about in their text but what their graphs clearly show is the following caveat: UC patients with a low relative Candida abundance at baseline did not only not clinically benefit from the FMT, but their dysbiosis, inflammation and Candida levels post-FMT was mostly even larger than before (confounders? Small sample size?):
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