Gut Microbiome Recovery in Clostridioides difficile Infection Patients Receiving Multi-Strain Probiotics During Convalescence: A Prospective Pilot Series of Longitudinal Dynamics

Background/Objectives: Clostridioides difficile infection (CDI) is a major healthcare-associated infection associated with profound antibiotic-induced gut microbiome disruption that frequently persists after clinical resolution. This pilot study aimed to characterize early post-infectious gut microbiome recovery following an inaugural CDI episode and to descriptively assess microbiome remodeling during adjunctive multi-strain probiotic supplementation. Methods: Adult patients with mild-to-moderate CDI were prospectively enrolled after completing standard antimicrobial therapy and received a 30-day course of a high-potency, 10-strain probiotic formulation. Stool samples were collected before and after supplementation and analyzed using 16S rRNA gene sequencing with microbiome-inferred functional profiling, alongside targeted screening for enteric protozoa and yeasts. Results: Five patients completed paired analyses. At baseline, all patients exhibited severe dysbiosis characterized by markedly reduced microbial diversity, depletion of Actinobacteria and short-chain fatty acid-producing taxa, expansion of Proteobacteria, and unfavorable inferred metabolic signatures. After supplementation, four of five patients were observed to exhibit increased microbial diversity and partial improvement in global dysbiosis indices. Microbiome recovery was heterogeneous and non-linear, involving variable reductions in Proteobacteria, recovery of Actinobacteria, or both, with incomplete normalization of taxonomic balances and inferred functions. Enterotype shifts were observed in three patients, consistent with ecological reorganization rather than full restoration. Baseline protozoal colonization resolved in affected patients, while fungal dynamics showed clearance or species-level replacement. No early CDI recurrences were observed during follow-up. Conclusions: Interpretation is limited by the single-arm design without a control group, which precludes distinguishing supplementation-associated changes from natural post-antibiotic recovery. Even so, our findings highlight the complexity and inter-individual variability of early post-CDI microbiome recovery and support further investigation of integrative microbiome profiling to describe post-infectious dysbiosis dynamics.