Introduction

Small intestinal bacterial overgrowth (SIBO) is frequent in patients with past or active upper GI cancer. SIBO is associated with clinical symptoms including, bloating and diarrhea that may impact negatively on quality of life. Current treatment of SIBO is empirical and relies on the cyclical use of antibiotics.

Aims & Methods

The aim of the present study was to characterize the microbiome composition of patient with upper GI cancer with or with no SIBO.
From April 2021 to May 2022, consecutive patients with past or active GI cancer attending our oncology outpatient department were enrolled in a prospective case control study. Treatment naïve patients with a first diagnosis of upper GI cancer but no SIBO-related symptoms served as controls. All included patients completed a standardised questionnaire about SIBO-related symptoms (bloating, diarrhoea), concomitant medications, and quality of life. They were offered upper endoscopy with duodenal aspirate, provided a 30-day period with no antibiotic intake. SIBO was defined as a bacterial count greater than 10³ colony forming units per millilitre in the duodenal aspirate. Using optimized protocol, the DNA from duodenal aspirate was extracted and the V1-V2 region of the 16S rRNA gene was amplified by PCR and sequencing using the Illumina platform. Dedicated bioinformatical approach was used for the multifactorial sample analysis.

Results

The microbiome composition was analyzed in 7 controls, 17 patients with SIBO and 12 with no SIBO.
We detected 513 phylotypes from 71 genera belonging to 11 phyla in the duodenal aspirate. The most abundant genera were Streptococcus, Veillonella and Prevotella. All three groups differed significantly in terms of their microbiome at phylum level (PERMANOVA p < 0.05). Based on the analysis of the individual phyla, we were able to show that the abundance of Proteobacteria was significantly higher in the SIBO group (Kruskal-Wallis test p < 0.05). Correlation analyses revealed an association between bacterial abundance and clinical phenotype. For instance, Proteobacteria, correlated positively with diarrhea intensity (Spearman r=0.35, p= 0.0362), and that Bacteroidetes correlated negatively with the reduction in quality of life (Spearman r=-0.4525, p=0.0056). Within the overall cohort, we were able to identify two clusters characterized by different microbial composition, underlying malignant diseases and clinical symptoms.

Conclusion

Among patients with upper GI cancer, the microbiome composition of the duodenal aspirate of patients with SIBO was different compared to patients with no SIBO and controls. Microbiome composition profiling may offer the opportunity for a personalized treatment in patients with SIBO.