Culturomics-Guided Precision FMT Enables Stable Antibiotic-Independent Engraftment via Metabolic Niche Targeting

Culturomics-guided, niche-targeted FMT enables stable antibiotic-independent engraftment for over 72 days by filling vacant metabolic niches in recipient mouse microbiomes.

• Why it matters: Current FMT does not use metabolic niche information to guide donor-recipient matching, leaving engraftment vulnerable and limiting mechanistic precision.
• What they did: Using a panel of 60 media conditions, the study profiles metabolic niche landscapes in genetically identical mice and identifies niche-associated communities (NACs) that target vacant versus occupied recipient niches after antibiotic pretreatment or none.
• The result: Antibiotic pretreatment compromises resilience, while NACs targeting vacant niches persist for over 72 days without antibiotic pretreatment and reshape native communities more with complex NACs than simpler ones.