Abstract

Clostridioides difficile is a pathogen found in the gut that can proliferate once antibiotics remove its competing bacteria, leading to recurrent Clostridioides difficile infection (rCDI). Fecal microbiota transplantation (FMT) treats rCDI by restoring a donor's balanced gut microbiota in the patient. Since bacterial strains within the same species can behave differently, confirming that a bacterium detected in the patient after treatment is the same strain that came from the donor, rather than a different strain of the same species that was already present, requires strain-level resolution rather than species-level identification alone.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• How can shared microbial strains between metagenomic samples be identified?
• What information is needed to determine whether two samples share the same strain rather than just the same species?
• How can shared strain patterns show donor engraftment and strain persistence in fecal microbiota transplantation (FMT)?

Learning Objectives

• Run the SameStr workflow in Galaxy to detect shared microbial strains across metagenomic samples
• Explain the role of each tool in the SameStr workflow
• Interpret the shared strain outputs produced by SameStr Summarize
• Distinguish between strain engraftment and persistence in FMT-treated samples based on SameStr's output