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Updated: May 13, 2025

Murine Fecal Isolation and Microbiota Transplantation
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Metagenomic source tracking after microbiota transplant therapy.

Susan L Hoops1,2, Daphne Moutsoglou3,4, Byron P Vaughn4,5

  • 1Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.

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|April 14, 2025
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Summary

A new pipeline, MAGEnTa, accurately assesses donor microbial engraftment in microbiota transplant therapies (MTTs). It reliably tracks bacterial strains, even with ambiguous DNA, advancing MTT development.

Keywords:
Metagenomicsfecal microbiota transplantmetagenome-assembled genomemicrobiota engraftmentmicrobiota transplant therapyshotgun sequencingulcerative colitiswhole-genome sequencing

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Area of Science:

  • Microbiome research
  • Genomics
  • Bioinformatics

Background:

  • Assessing donor microbial engraftment is crucial for microbiota transplant therapies (MTTs).
  • Current methods struggle to distinguish donor DNA from patient DNA, limiting engraftment analysis.
  • Metagenome-assembled genomes (MAGs) offer strain-level tracking but face ambiguity challenges.

Purpose of the Study:

  • To introduce MAGEnTa, a novel, cost-efficient bioinformatics pipeline for accurate donor microbial engraftment assessment.
  • To enable reliable tracking of individual bacterial strains post-microbiota transplant therapy.
  • To overcome limitations in distinguishing donor-derived DNA from patient-derived DNA.

Main Methods:

  • Developed MAGEnTa, a pipeline using donor and pre-treatment MAGs for comparison.
  • Employed Bayesian statistics to resolve ambiguous DNA reads aligning to both donor and patient samples.
  • Validated MAGEnTa using simulated datasets and a clinical trial dataset for ulcerative colitis.

Main Results:

  • MAGEnTa demonstrated high accuracy in recovering engrafted strains with minimal errors in simulated data.
  • The pipeline proved robust even with shallow sequencing depths.
  • Results from a clinical trial dataset were consistent with 16S rRNA gene SourceTracker analysis, providing enhanced MAG-level specificity.

Conclusions:

  • MAGEnTa is a powerful and cost-efficient tool for studying microbial community and strain engraftment dynamics.
  • The pipeline enhances the development of microbiota transplant therapies by providing precise engraftment analysis.
  • MAGEnTa can be integrated into broader functional and taxonomic analysis frameworks for microbiome research.