Patients with concurrent Helicobacter pylori infection and small intestinal bacterial overgrowth (SIBO) represent a clinically challenging subgroup, often experiencing refractory gastrointestinal symptoms and diminished treatment responses. Current evidence indicates that individuals infected with H. pylori may related SIBO as a comorbidity; however, the synergistic effects of these conditions on gut ecosystem homeostasis remain poorly understood. To address this knowledge gap, we employed a dual-omics approach that combined shotgun metagenomic sequencing with liquid chromatography-mass spectrometry (LC-MS) metabolomic profiling. This methodology allowed for a comprehensive mapping of microbial community structures, including species-level taxonomy and functional pathways, as well as host-microbiota co-metabolism signatures in fecal samples.

Patients presenting with concurrent Helicobacter pylori infection and small intestinal bacterial overgrowth (SIBO) constitute a clinically challenging subgroup characterized by refractory gastrointestinal symptoms and diminished responses to standard therapeutic interventions. Current evidence supports an association between H. pylori infection and an increased prevalence of SIBO as a comorbidity. However, the synergistic effects of these two conditions on the fundamental mechanisms governing gut ecosystem homeostasis - particularly concerning microbial community dynamics, functional metabolic output, and host-microbial interactions - remain poorly understood, representing a significant knowledge gap.

To systematically address this gap and elucidate the complex interplay, we implemented an integrated dual-omics analytical approach. This methodology combined shotgun metagenomic sequencing of fecal samples with liquid chromatography-mass spectrometry (LC-MS) metabolomic profiling. This powerful combination enables a comprehensive mapping of the gut ecosystem by simultaneously characterizing: Host-Microbiota Co-Metabolism Signatures: Revealing the metabolic landscape through the detection and quantification of metabolites derived from microbial activity, host metabolism, and crucially, their interactions (co-metabolism) within the fecal metabolome.

This multimodal strategy offers an unprecedented, holistic view of the perturbations induced by the co-occurrence of H. pylori infection and SIBO, moving beyond singular aspects to capture the integrated functional and compositional state of the gut ecosystem.

Inclusion Criteria:

• Age from 18 to 65 years;
• All enrolled patients underwent both the 13C-urea breath test (13C-UBT) and hydrogen-methane breath test (HMBT).

Exclusion Criteria:

• Coexistence of significant concomitant illnesses, including heart disease, renal failure, hepatic disease, previous abdominal surgery, lactation, or pregnancy;
• Patients who had used probiotics and antibiotics in the past 12 weeks;
• Unwillingness to participate in this study.

A prospective observational cohort of adult patients (aged 18-65 years) with concomitant Helicobacter pylori infection and small intestinal bacterial overgrowth (SIBO) was enrolled at Zhongshan Hospital (Xiamen), Fudan University.