Figure 1.

Mutualistic bacteria utilise amino acids and soluble carbohydrates as a source of energy, competing with potential pathogens. A layer of mucus, comprised of glycoproteins produced by goblet cells, lines the intestinal mucosa. This prevents potential pathogens from attaching to the intestinal epithelium by acting as a physical barrier. Many symbionts fortify the mucosal barrier, inhibiting pathogen outgrowth. Other bacteria can directly inhibit pathogens using the type VI secretion system (T6SS) or by secreting antimicrobial compounds such as bacteriocins, pheromone peptides and short-chain fatty acids (e.g., acetic, butyric and propionic acids). Others possess bile salt hydrolases that deconjugate bile acids or convert them from primary to secondary bile acids, which are able to inhibit the growth of pathogens. A range of symbionts induces the production of cytokines, such as IL-22 and IL-1β, which protect against colonisation by pathogens. Indigenous microbiota shape and modulate innate and adaptive immune responses. Interactions between bacteria and epithelial cells contribute to the regulation of epithelial permeability through the modulation of tight junctions. Diverse gut microbiota maintain optimal homeostasis but can be disrupted by antimicrobials and other drugs. This results in significant alterations in structure and function and permits the emergence of niches that pathogens can occupy.