Bacterial viability in faecal transplants: Which bacteria survive?

Area of Science:

• Microbiology
• Gastroenterology
• Immunology

Background:

• Faecal microbiota transplantation (FMT) shows therapeutic promise for inflammatory conditions.
• The mechanisms of FMT benefit are not fully understood, but microbial viability is considered crucial.
• Standard FMT preparation protocols may compromise the viability, diversity, and function of transplanted microbes.

Purpose of the Study:

• To investigate the impact of common faecal transplant preparation methods on microbial viability.
• To assess how anaerobic, ambient air, and freeze-thaw processing affects microbial composition and function.

Main Methods:

• Stool samples from eight donors were processed under anaerobic, ambient air, and freeze-thaw conditions.
• Propidium monoazide (PMA) treatment combined with qPCR and 16S rRNA gene sequencing assessed viable microbiota.
• Short-chain fatty acid (SCFA) analysis determined the functional potential of the processed samples.

Main Results:

• Processing in ambient air reduced bacterial viability to 19%, significantly decreasing key anaerobic commensals like Faecalibacterium prausnitzii.
• Ambient air exposure led to up to 12-fold reductions in beneficial taxa and impaired short-chain fatty acid (SCFA) biosynthesis (butyrate, acetate).
• Freeze-thaw processing reduced overall viable bacteria but did not significantly alter microbial composition.

Conclusions:

• Preparing faecal material in ambient air drastically reduces viable anaerobic microbes and their metabolic functions.
• This processing method compromises the anti-inflammatory potential of faecal transplants by reducing key metabolite production.
• Optimized preparation protocols are essential to preserve the integrity and efficacy of faecal microbiota transplantation.