Pathogenic bacteria in the intestinal lumen

Pathogenic bacteria in the intestinal lumen refer to a diverse group of harmful microorganisms, such as Salmonella, Escherichia coli, and Clostridioides difficile, that colonize the gastrointestinal tract and cause disease [Frontiers in Microbiology, 2023]. These pathogens disrupt the normal gut microbiota and the intestinal mucosal barrier, leading to conditions ranging from acute gastroenteritis to chronic inflammatory diseases and systemic sepsis [NIH, 2021; World Journal of Gastroenterology, 2025]. In clinical practice, they are the primary targets for antimicrobial agents, including non-absorbable antibiotics like rifaximin and fidaxomicin, which aim to reduce the pathogen load directly within the gut [Frontiers in Immunology, 2025]. Additionally, therapeutic strategies such as probiotics and fecal microbiota transplantation (FMT) are employed to outcompete these pathogens and restore microbial balance through competitive exclusion and immune modulation [PLOS ONE, 2009; Animals, 2024]. Monitoring these pathogens often involves stool-based assays, PCR for specific toxins, and biomarkers of intestinal damage like fecal calprotectin or D-lactate [NIH, 2023]. However, targeting these bacteria carries significant safety risks, including the development of multi-drug resistance and the depletion of beneficial commensal populations, which can lead to secondary infections like Clostridioides difficile overgrowth [Frontiers in Immunology, 2025].

Other names

Enteric pathogensIntestinal pathogensGut pathogensPathogenic gut microbiota

Antibiotics target bacterial cell wall synthesis, protein synthesis, or DNA replication; probiotics exert competitive exclusion, produce antimicrobial substances, and modulate host immunity.