Examining spatial microbiome variations across gastrointestinal tract regions in obesity

Obesity, a global health concern, is associated with alterations in the gut microbiome, yet its spatial dynamics across the gastrointestinal (GI) tract remain poorly understood. This study provides the first comprehensive analysis of the spatial microbiome in individuals with obesity, encompassing samples from the stomach, peritoneum, jejunum (50 cm and 150 cm post-Treitz), and feces before and after bariatric surgery. Using 16 S rRNA sequencing, we analyzed microbial composition and diversity after computational decontamination in 172 high-quality samples from 51 participants. Our results reveal significant differences in alpha diversity across GI sites, with stool samples exhibiting the highest diversity, which decreased post-surgery. The presence of microbial DNA in traditionally sterile compartments, such as the peritoneum and stomach, suggests potential microbial-host interactions warranting further exploration. Contaminants, including Nitrotoga sp., were identified in low-biomass samples and excluded using computational decontamination, emphasizing the need for rigorous controls. This study establishes a foundation for spatial microbiome analysis in obesity, highlighting the impact of bariatric surgery and the importance of advanced multi-omics approaches to unravel host-microbiome dynamics.