Being a better version of yourself: genetically engineered probiotic bacteria as host defense enhancers in the control of intestinal pathogens

Abstract

Intestinal pathogens pose a significant global health burden, and traditional antibiotic treatments often disrupt the beneficial gut microbiota that plays a crucial role in maintaining host health through pathogen prevention and immune regulation. Although probiotics have emerged as promising therapeutic agents, their efficacy is limited by strain-dependent variations, survival challenges in the gastrointestinal tract, and inconsistent immune responses. Recent advances in genetic engineering, particularly CRISPR-Cas systems and their combinations with complementary technologies, such as Cre-lox and RecE/T, have enabled the precise modification of probiotic strains to enhance their therapeutic potential. These enhanced probiotics demonstrate improved functionality through multiple mechanisms, including increased adhesion via the expression of specific proteins (InlA, FnBPA, and LAP), targeted antimicrobial activity through engineered sensing systems (Lactococcus lactis detecting Vibrio cholerae CAI-1), and enhanced immunomodulation through cytokine production. Results have demonstrated the potential of genetically modified probiotics in preventing and treating gastrointestinal infections through mechanisms that include competitive exclusion, bacteriocin production, intestinal barrier reinforcement, and immune modulation. However, challenges remain in ensuring genetic stability and preventing horizontal gene transfer. Future research should focus on optimizing probiotic strains for targeted applications while addressing biosafety concerns. By understanding the complex interplay between probiotics, pathogens, and host immunity, innovative strategies can be developed to harness the full therapeutic potential of probiotic interventions in maintaining gut health.

Keywords: CRISPR-Cas; Probiotics; biosafety; gastrointestinal pathogens; genetic modification; gut health; microbiome.

Figure 1.

Mechanisms of probiotic bacteria against pathogens. each color represents a different strategy of the gut microbial community to fight against pathogenic species of bacteria. Examples of possible genetic modifications that may contribute to more efficient utilization of the described mechanisms are shown in bubbles in corresponding colors. All of the presented mutations are described in more detail in further chapters of the review.

Figure 2.

Limitations of conventional probiotics. administration of probiotics, especially engineered ones, to patients has its limitations, some of them include: (A) possibility of HGT between probiotics and pathogens, which may result in aiding pathogens, (B) overgrowth of genetically modified probiotics, and thus microbial imbalance, (C) possibility of probiotics to survive the stomach acid conditions in insufficient number to colonize the gut, (D) antibiotic resistance, that can be spread in the population of other gut bacteria, both beneficial and pathogenic, (E) DNA instability, that can result in losing the introduced mutation, or gain of unsolicited one, (F) interactions with gut microbiota, that may result in disrupting homeostasis, (G) gain of pathogenic activity by administered probiotics.