Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT

Area of Science:

• Microbiology
• Gastroenterology
• Immunology

Background:

• Probiotics are commonly used to prevent antibiotic-induced gut dysbiosis.
• The effect of probiotics on the recovery of the gut mucosal microbiome niche post-antibiotics is not well understood.

Purpose of the Study:

• To investigate the impact of probiotics and autologous fecal microbiome transplantation (aFMT) on the reconstitution of the gut mucosal microbiome niche after antibiotic treatment in mice and humans.

Main Methods:

• Invasive examination of murine and human mucosal microbiomes.
• Comparison of spontaneous recovery, probiotic intervention, and aFMT.
• In vitro analysis of Lactobacillus-secreted factors.
• Host transcriptome analysis.

Main Results:

• Antibiotics enhanced probiotic colonization in human mucosa but not in mice.
• Probiotics delayed and incompletely restored the indigenous microbiome and host transcriptome compared to spontaneous recovery.
• aFMT rapidly and nearly completely restored the microbiome and transcriptome within days.
• Lactobacillus-secreted factors inhibited microbiome recovery in vitro.

Conclusions:

• Probiotic use post-antibiotics may compromise gut mucosal recovery and microbiome recolonization.
• aFMT demonstrates superior efficacy in restoring the gut microbiome and host transcriptome after antibiotic perturbation.
• Development of aFMT or personalized probiotics is needed to support mucosal healing without hindering microbiome recovery.