Metagenomic and Metabolomic Signatures of Gut Microbiota After Helicobacter pylori Eradication Therapy Supplemented with Butyric Acid and Inulin: Observational Study.
Abdulkhakov S, Safina D, et al. • International journal of molecular sciences • 2026
Bismuth-based quadruple H. pylori eradication therapy supplemented with butyrate and inulin promotes persistent microbial reorganization, with observed recovery unlikely to be spontaneous and probably reflecting the protective effect of butyrate and inulin supplementation.
Key Findings
Results
Helicobacter pylori eradication therapy caused a significant decrease in the relative abundance of Actinobacteria, including Bifidobacterium and Collinsella.
Fecal samples were collected from 15 patients aged 19-64 years at three timepoints: prior to treatment, immediately after treatment, and one month after therapy.
The decrease in Actinobacteria was observed immediately after the therapeutic intervention.
Bifidobacterium and Collinsella were specifically identified as the affected genera within the Actinobacteria phylum.
The bismuth-based quadruple therapy was supplemented with butyrate and inulin.
Results
Faecalibacterium prausnitzii levels remained consistent while Roseburia faecis levels exhibited a substantial decline following eradication therapy.
Both Faecalibacterium prausnitzii and Roseburia faecis are key butyrate-producing bacteria.
The decline in Roseburia faecis was interpreted as suggesting a disruption in key butyrate-producing bacteria.
The stability of Faecalibacterium prausnitzii levels may potentially reflect a partial protective effect of supplementation.
These findings were based on metagenomic profiling of fecal samples from 15 patients.
Results
A moderate increase in the relative abundance of opportunistic Proteobacteria, Firmicutes, and Bacteroides was observed after eradication therapy.
The increase in opportunistic bacteria was characterized as 'moderate' by the authors.
Proteobacteria, Firmicutes, and Bacteroides were all identified as increased phyla.
These shifts were detected through metagenomic profiling.
The microbial shifts persisted for a period of four weeks following therapy.
Results
Fecal butyric acid concentration declined in response to eradication therapy but returned to baseline levels within one month.
Short-chain fatty acids (SCFAs) were measured through metabolomic profiling of fecal samples.
Butyric acid showed a decline immediately after therapy followed by recovery to baseline levels at the one-month timepoint.
The recovery pattern was observed at the one-month post-therapy collection timepoint.
The authors suggest the recovery is unlikely to be spontaneous and probably reflects the protective effect of butyrate and inulin supplementation.
Results
Fecal valeric acid levels declined following eradication therapy with no tendency for recovery over the one-month follow-up period.
Valeric acid was one of the short-chain fatty acids measured through comprehensive metabolomic profiling.
Unlike butyric acid, valeric acid showed no tendency to increase after the one-month course of therapy.
This persistent decline distinguished valeric acid from butyric acid in terms of recovery trajectory.
The study followed patients for a total of one month post-therapy, which may be insufficient to observe potential later recovery.
Results
Microbial and metabolic shifts induced by eradication therapy persisted for at least four weeks following the completion of treatment.
The persistence of shifts was noted across both metagenomic and metabolomic measurements.
The four-week duration covered the entire post-therapy follow-up period of the study.
The authors conclude that 'H. pylori eradication therapy intervention promotes a persistent microbial reorganization.'
The authors note that larger sample sizes and longer-duration studies are required to confirm these conclusions.
The study was limited to 15 patients, which the authors acknowledge as a limitation.
What This Means
This research suggests that the standard antibiotic-based treatment used to eliminate Helicobacter pylori (a stomach bacterium linked to ulcers and stomach cancer) causes meaningful disruptions to the community of bacteria living in the gut. The study tracked 15 patients before treatment, immediately after completing a two-week course of bismuth-based quadruple therapy (which included four antimicrobial agents plus butyrate and inulin supplements), and again one month later. The researchers found that beneficial bacteria — particularly those that produce a health-promoting compound called butyric acid — were significantly reduced after treatment, while some potentially harmful bacteria increased moderately.
On the positive side, butyric acid levels in the stool did eventually return to near-normal levels within a month, and one important butyrate-producing bacterium (Faecalibacterium prausnitzii) remained relatively stable throughout. However, another type of short-chain fatty acid called valeric acid stayed low even a month after treatment, and some bacterial disruptions persisted throughout the entire follow-up period. The authors suggest that the partial recovery observed may not have happened on its own, and instead may be due to the butyrate and inulin supplements that were given alongside the antibiotics.
This research matters because H. pylori eradication therapy is one of the most commonly prescribed antibiotic regimens worldwide, and understanding its effects on gut health is important for optimizing treatment approaches. The findings suggest that adding gut-supportive supplements like butyrate and inulin to standard eradication therapy may help protect the gut microbiome during and after antibiotic treatment. However, the study was small (15 patients) and only followed patients for one month, so the authors caution that larger and longer studies are needed before firm conclusions can be drawn.
Abdulkhakov S, Safina D, Markelova M, Ponomareva E, Siniagina M, Khusnutdinova D, et al.. (2026). Metagenomic and Metabolomic Signatures of Gut Microbiota After Helicobacter pylori Eradication Therapy Supplemented with Butyric Acid and Inulin: Observational Study.. International journal of molecular sciences. https://doi.org/10.3390/ijms27198485