Potential subtype-specific alterations in gut microbiota and branched-chain amino acid metabolism in hydrogen- and methane-predominant small intestinal bacterial overgrowth

We aimed to investigate the clinical, microbiome, and metabolomic characteristics of hydrogen (H₂)- and methane (CH₄)-predominant small intestinal bacterial overgrowth (SIBO) subtypes. We retrospectively enrolled adults who underwent standardized lactulose hydrogen–methane breath testing between February 2021 and July 2025. Participants were categorized as Normal, H₂–SIBO, CH₄–SIBO, or mixed H₂/CH₄–SIBO. Clinical characteristics were compared using Kruskal–Wallis tests and chi-square tests. Multivariable logistic regression was used to identify factors independently associated with each SIBO subtype. Expiratory gas profiles (AUC, peak, and mean values) were quantified, and correlations with age and body mass index (BMI) were assessed using Spearman analysis. In a subset of participants, stool samples underwent 16S rRNA gene sequencing and untargeted metabolomic profiling, followed by integrative analyses of microbiota composition, diversity, and metabolic signatures across SIBO subtypes. Among 503 participants, higher serum albumin levels were independently associated with H₂–SIBO, whereas higher fasting glucose was independently associated with CH₄–SIBO. Breath-test profiling indicated that methane parameters, rather than hydrogen, better differentiated SIBO subtypes, and total (H₂ + CH₄) gas output was modestly correlated with age but not BMI. In the exploratory multi-omics subset, fecal microbiota composition and metabolomic signatures differed by subtype; LEfSe identified Bacteroidaceae as a CH₄-SIBO signature and Alcaligenaceae/Acidaminococcaceae as H₂–SIBO signatures. Differential metabolites were enriched in pathways related to branched-chain amino acid biosynthesis, lipid metabolism, and mineral absorption. H₂- and CH₄-predominant SIBO subtypes exhibit distinct clinical correlates and stool microbiome–metabolome profiles. Methane exhalation appears more informative for differentiating subtypes, and age is modestly associated with total expiratory gas volumes. These findings support potential subtype-specific host–microbe metabolic interactions, although the multi-omics results should be interpreted as exploratory.