The most notable disruptions were seen in Donor 1, who underwent a longer course of antibiotics and showed significant changes in microbial diversity, composition, functionality, and ARG profiles that persisted even 8 months post-treatment. In contrast, Donor 2 exhibited relative compositional stability between 7 and 15 months after treatment. These findings suggest that in cases of prolonged antibiotic exposure, microbiota recovery may take up to 8 months or longer. Conversely, for shorter antibiotic courses, an 8-month window may represent a reasonable timeframe for microbiota recovery and donor requalification.
Our study revealed that antibiotic exposure leads to reduction or near complete disappearance of specific SCFA producers like Bifidobacterium bifidum, Roseburia inulinivorans, Eubacterium hallii, and Akkermansia muciniphila. In one donor, this disruption extended beyond microbiota composition, affecting metabolic pathways, including the biosynthesis of essential amino acids like L-arginine and L-methionine, which are particularly underrepresented in IBD patients.
Even when the abundance of some bacteria remains relatively unchanged, shifts in their strain communities, as seen with Bacteroides massiliensis and Bacteroides xylanisolvens, may still impact their functionality. These strain-level shifts underscore the complexity of microbial recovery following antibiotic exposure, as even subtle variations in strain composition can lead to significant changes in functional capacity.
the depletion of Bifidobacterium bifidum, critical for glycogen degradation, underscores the risks posed by the loss of beneficial strains. Moreover, our findings indicate that functional contributions stem not only from bacterial species with altered strains but also from those whose strains remained stable in abundance. For example, pathways such as thiamine biosynthesis and O-antigen building blocks biosynthesis were influenced by bacteria like Bifidobacterium adolescentis, Faecalibacterium prausnitzii, and Roseburia faecis, which remained relatively stable in their abundances post-antibiotic treatment. However, despite their stable population levels, changes in the surrounding microbial community likely altered their relative functional contributions. Such dynamics suggest that stable taxa can adapt their metabolic outputs in response to environmental changes, including those induced by antibiotic exposure.
We observed reduced viral diversity in donor samples following antibiotic exposure. Viruses, particularly bacteriophages, play an integral role in shaping bacterial fitness and maintaining gut homeostasis.
its sustained high levels, even 8 months or more after antibiotic exposure, indicate that recovery of the virome to a pre-treatment state may be incomplete
This persistence suggests a shift in host-bacteriophage dynamics
RNA viruses were not captured, which likely contributed to the low number of detected viral species. Future studies incorporating RNA sequencing methodologies, such as metatranscriptomics, would be necessary to provide a more comprehensive characterization of the gut virome
the impact of antibiotic exposure on donor microbiota was more pronounced than anticipated, with lasting and complex changes, particularly in key bacterial species and their functionality. These changes could potentially affect the efficacy of FMT, especially in indications beyond rCDI, and suggest that donor microbiota performance post-antibiotic treatment may be unpredictable. Therefore, donor suspension periods may need to be individualized, taking into account the spectrum of antibiotics, treatment duration, and other host-specific factors.
