Abhinaya Muruganandham

Background.  Fecal microbiota transplantation (FMT) is a transformative therapy for restoring gut microbial ecology, particularly in treating recurrent Clostridioides difficile infection (rCDI) [1,2,3,4]. While highly successful for rCDI, its efficacy varies in other conditions like inflammatory bowel disease (IBD) or antibiotic-associated diarrhea [4]. Antibiotics significantly disrupt intestinal ecology, leading to diversity loss and antibiotic resistance[2,5]. Understanding microbial engraftment, how donor strains colonize and persist in the recipient, is critical for evaluating FMT success [3]. Currently, a gap exists in standardizing a genomic detection methodology that can accurately track these strains at a high resolution. Traditional methods often fail to distinguish between multiple coexisting strains of the same species, which is essential for determining if recovery is driven by donor engraftment or the resilience of the recipient’s indigenous microbiota [6, 3].

Methods.  Literature review was conducted through a PubMed database search using the keywords “Fecal Microbiota Transplantation,” “genomic detection methodology,” and “post-antibiotic recovery.” Results were filtered from 2020-2026.

Results.  Key findings indicate that while 16S rRNA sequencing provides a broad taxonomic overview, it lacks the resolution to track specific donor strains necessary for assessing engraftment [4]. Short-read shotgun metagenomics improves this by enabling strain-level profiling through single-nucleotide polymorphisms (SNPs), revealing that higher donor strain engraftment correlates with clinical success (P=0.017) [3, 7]. However, long-read metagenomics emerged as the most effective methodology. It demonstrates superior precision and specificity by resolving de novo metagenomic assemblies even when multiple strains of the same species co-exist [8,6]. Furthermore, long-read sequencing allows for the assessment of genomic and epigenomic stability in engrafted strains over longer periods up to five years [6].

Conclusions. Long-read metagenomics is the most effective methodology for assessing FMT efficacy, offering high resolution for tracking donor strain engraftment and stability [6]. These findings imply that clinical practice should transition toward high-resolution genomic tracking to personalize FMT protocols and ensure long term ecological recovery. Future research should investigate the functional adaptations of engrafted strains and develop defined bacterial consortia as safer alternatives to full-spectrum FMT [1,9].

Works Cited

1. Chng KR, Ghosh TS, Tan YH, Nandi T, Lee IR, Ng AHQ, et al. Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut. Nat Ecol Evol 2020;4:1256–67. https://doi.org/10.1038/s41559-020-1236-0.

2. Lathakumari RH, Vajravelu LK, Satheesan A, Ravi S, Thulukanam J. Antibiotics and the gut microbiome: Understanding the impact on human health. Medicine in Microecology 2024;20:100106. https://doi.org/10.1016/j.medmic.2024.100106.

3. Ianiro G, Punčochář M, Karcher N, Porcari S, Armanini F, Asnicar F, et al. Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases. Nat Med 2022;28:1913–23. https://doi.org/10.1038/s41591-022-01964-3.

4. Wang L, Guo G, Xu Y, Li L, Yang B, Zhao D, et al. The effect of fecal microbiota transplantation on antibiotic-associated diarrhea and its impact on gut microbiota. BMC Microbiol 2024;24. https://doi.org/10.1186/s12866-024-03261-0.

5. Karimianghadim R, Satokari R, Yeo S, Arkkila P, Kao D, Pakpour S. Prolonged effect of antibiotic therapy on the gut microbiota composition, functionality, and antibiotic resistance genes’ profiles in healthy stool donors. Front Microbiol 2025;16. https://doi.org/10.3389/fmicb.2025.1589704.

6. Fan Y, Ni M, Aggarwala V, Mead EA, Ksiezarek M, Cao L, et al. Long-read metagenomics for strain tracking after faecal microbiota transplant. Nat Microbiol 2025;10:3258–71. https://doi.org/10.1038/s41564-025-02164-8.

7. Bars-Cortina D, Ramon E, Rius-Sansalvador B, Guinó E, Garcia-Serrano A, Mach N, et al. Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota. BMC Genomics 2024;25. https://doi.org/10.1186/s12864-024-10621-7.

8. Benoit G, James R, Raguideau S, Alabone G, Goodall T, Chikhi R, et al. High-quality metagenome assembly from nanopore reads with nanoMDBG. Nat Commun 2026;17. https://doi.org/10.1038/s41467-026-69760-y.

9.  Ronkainen A, Khan I, Krzyżewska-Dudek E, Hiippala K, Freitag TL, Satokari R. In vitro adhesion, pilus expression, and in vivo amelioration of antibiotic-induced microbiota disturbance by Bifidobacterium spp. strains from fecal donors. Gut Microbes 2023;15. https://doi.org/10.1080/19490976.2023.2229944.