The gastric ecosystem: assessing resident microbiome vs. transient microorganisms in obesity and following bariatric interventions

Long considered a sterile environment due to its acidity, the stomach is increasingly recognized as a low-biomass but structured microbial ecosystem. Advances in culture-independent sequencing reveal a diverse gastric microbiome shaped by acid secretion, mucosal physiology, diet, medication use, and Helicobacter pylori colonization, although distinguishing metabolically active residents from transient oropharyngeal or dietary microorganisms remains a significant challenge. In healthy individuals, gastric mucosal communities primarily consist of Bacillota, Pseudomonadota, Actinomycetota, Bacteroidota, and Fusobacteriota, with genera such as Streptococcus, Prevotella, Rothia, and Veillonella consistently detected. Obesity is associated with altered gastric physiology, including higher pH, delayed emptying, and increased bile reflux, alongside distinct microbial signatures. Helicobacter pylori remains a dominant ecological factor modifying acidity, inflammation, and niche structure, while proton-pump inhibitors significantly "oralize" the gastric microbiome. Although animal models suggest that bariatric surgery can remodel the gastric microbiome, no human study has yet characterized gastric microbial changes following sleeve gastrectomy, gastric bypass, or endoscopic bariatric therapies, leaving the translational relevance of preclinical findings uncertain. Given the central role of the stomach in nutrient sensing and metabolic hormone secretion, its microbial ecosystem warrants dedicated investigation.