Intestinal bacterial pathogens and gut microbiota

The intestinal bacterial pathogens and gut microbiota represent a complex ecosystem of trillions of microorganisms, including bacteria, viruses, and fungi, that inhabit the human gastrointestinal tract (Wikipedia, 2024; PMC, 2019). This community is essential for host health, performing critical functions such as the metabolism of dietary fibers into short-chain fatty acids (SCFAs), synthesis of vitamins K and B12, and the maturation of the host immune system (NIH, 2015; PMC, 2021). A primary protective role of the gut microbiota is colonization resistance, where commensal bacteria prevent the invasion and overgrowth of enteric pathogens like Clostridioides difficile and Salmonella through nutrient competition and the secretion of antimicrobial peptides (Royal Society, 2017; PMC, 2022). Disruptions to this microbial balance, termed dysbiosis, are associated with a wide range of pathologies, including inflammatory bowel disease (IBD), colorectal cancer, and metabolic disorders like obesity (PMC, 2019; PMC, 2021). Therapeutic interventions targeting this system include narrow-spectrum antibiotics for specific pathogens, as well as microbiome-restoring therapies such as probiotics and fecal microbiota transplantation (FMT) (Patsnap, 2025; PMC, 2023). While these therapies offer significant potential, they also present challenges such as the risk of promoting antibiotic resistance and the potential for unintended systemic effects due to the complex, bidirectional interactions between the microbiota and host physiology (Yale, 2025; PMC, 2024).

Other names

Gut microbiomeIntestinal floraEnteric pathogensGastrointestinal microbiotaGut-associated microbes

Mechanisms of action include: 1) Inhibition of bacterial cell wall synthesis (e.g., vancomycin); 2) Disruption of DNA synthesis (e.g., metronidazole); 3) Inhibition of RNA polymerase (e.g., fidaxomicin) (PMC, 2023); 4) Competitive exclusion of pathogens by commensal bacteria; 5) Restoration of microbial diversity and ecological balance (e.g., FMT); and 6) Modulation of host-microbe metabolic signaling (Royal Society, 2017; PMC, 2022).