Modifications in gut microbiota composition in irritable bowel syndrome under the influence of probiotic therapy: next-generation sequencing-based analysis

Objective to evaluate the effectiveness of the probiotic Neoflorum in patients with irritable bowel syndrome (IBS) based on the dynamics of clinical symptoms and changes in gut microbiota composition, as determined by next‑generation sequencing (NGS). Materials and methods. This open‑label comparative study involved three male patients aged 50—53 years diagnosed with diarrhea‑predominant IBS. For 28 days, the patients received the probiotic Neoflorum at a dosage of 2 capsules per day during meals. Clinical condition was assessed throughout the study. Gut microbiota samples were collected before treatment and immediately after its completion. Metagenomic DNA sequencing was employed to investigate the microbial composition using high‑throughput NGS technology on the Ion GeneStudio S5 System platform (Thermo Fisher). The analysis utilized the Ion 16S Metagenomics Kit (ref 26216, LOT 2311034), IonCode Barcode Adapters (ref A36524), and Ion 540™ Kit‑Chef (ref A37865). Amplicon sequencing was performed targeting the 16S rRNA gene. Bioinformatic processing was conducted using Ion Reporter™ software and the dedicated Ion 16S™ metagenomic analysis module. Results. All patients had experienced IBS with diarrhea for at least one year. Before treatment, an imbalance in the microbiota was observed — specifically, an overabundance of Prevotellaceae and a deficiency of Faecalibacterium — accompanied by clinical symptoms such as abdominal pain, bloating, and defecation disorders. After the course of Neoflorum, beneficial modifications in microbiota composition were detected, including a reduction in pathogenic bacteria (Enterobacteriaceae) and an increase in microorganisms supporting gut barrier function and short‑chain fatty acid synthesis (Eubacterium rectale, Ruminococcus). Metabolic improvements were also noted: increased acetate and propionate production, reduced activity of ammonia‑producing bacteria and β‑glucuronidase. Clinically, this corresponded with a fourfold decrease in abdominal pain and a threefold reduction in diarrheal symptoms. No adverse effects associated with Neoflorum intake were reported. Conclusions. The use of NGS technology provided robust evidence of the beneficial impact of Neoflorum on gut microbiota composition. Neoflorum proved effective in managing diarrhea‑predominant IBS through its targeted action. The treatment led to microbiota normalization, reduction in inflammatory burden, and improvement in enzymatic activity and metabolic potential (protein and carbohydrate metabolism, decreased toxic load). Prolonged therapy for 1—2 months is recommended, accompanied by dietary monitoring and adjustment.