Engineered Phage Enables Continuous Protein Delivery in Gut

In recent years, the quest to develop effective oral delivery methods for biologic drugs has faced significant challenges, primarily due to the hostile environment of the upper gastrointestinal tract. Enzymatic degradation and acidic pH conditions often render orally administered biologics inactive before they can reach their therapeutic targets. Traditional strategies involving engineered microbes aimed at producing these biologics directly within the lower gastrointestinal tract encounter a formidable obstacle: fierce competition from resident commensal bacteria. A groundbreaking approach emerging from this bottleneck harnesses the power of bacteriophages—viruses that specifically infect bacteria—as vehicles for therapeutic protein delivery in the gut.

This innovative research leverages bacteriophage T4, a well-characterized virulent phage known to specifically infect nonpathogenic strains of Escherichia coli residing in the mammalian gut. Unlike lysogenic phages that integrate into bacterial genomes, virulent phages like T4 replicate rapidly and lyse their bacterial hosts, releasing progeny phage particles along with any heterologous proteins engineered into their genome. Exploiting this natural lytic cycle, researchers have engineered T4 phages capable of synthesizing and releasing therapeutic proteins locally within the gut environment, thereby circumventing the hostile conditions that plague conventional oral biologic administration.

A foundational challenge when reprogramming bacteriophages for heterologous protein production is balancing robust expression of the therapeutic proteins with maintenance of phage viability and infectivity. To address this, the researchers first conducted an exhaustive screening of T4-specific promoters, aiming to identify those with maximal protein expression yet minimal detrimental effects on phage replication and titers. Through meticulous promoter engineering, they isolated sequences that allowed high-level production of target proteins without compromising the phage’s lytic efficiency—an achievement key to sustained therapeutic protein delivery.

Armed with optimized genetic elements, the team engineered T4 phages to produce a serine protease inhibitor designed to temper the activity of a pro-inflammatory enzyme whose levels are elevated in ulcerative colitis. The choice of this therapeutic target reflects a nuanced understanding of disease pathology—where unchecked protease activity contributes to exacerbated inflammation and tissue damage. Upon administration in a mouse model of colitis, the engineered phages successfully infected resident E. coli populations, expressed the inhibitor protein in situ, and led to a measurable reduction in protease activity, indicating both functional expression and biological efficacy.

Notably, the therapeutic benefits extended beyond inflammatory bowel disease models. When applied to mouse models of diet-induced obesity, the engineered phages demonstrated a capacity to mitigate weight gain and systemic inflammation. This broadens the potential horizon for phage-mediated protein delivery as a versatile platform capable of addressing metabolic disorders and inflammation concurrently, both of which are often intertwined in complex disease contexts.

The technological leap demonstrated here lies in harnessing the existing microbiota as a living factory for sustained, localized drug synthesis, releasing therapeutic proteins directly at the site of disease action. Phage engineering in this context sidesteps the need to introduce foreign microbial strains that often fail to colonize efficiently or compete with established commensals. Instead, by targeting indigenous bacteria, the therapeutic intervention integrates seamlessly into the gut ecosystem.

Furthermore, the use of virulent phages ensures a controlled dynamic where infected bacteria are lysed upon therapeutic protein production, potentially limiting unchecked spread or long-term persistence of engineered bacteria in the host. This adds an inherent biosafety dimension to the approach, as the phage-bacteria dynamics self-regulate the duration and magnitude of therapeutic protein release.

The methodology described opens exciting avenues for synthetic biology and therapeutic microbiomics. Future work may explore the modularity of this platform by encoding diverse proteins targeting a range of gastrointestinal or systemic diseases, including enzymes, antibodies, or cytokine modulators. Tailoring phage host range to target other commensal species could further diversify applications to niche gut microenvironments.

Mechanistically, this system leverages the sophisticated interplay of phage biology and microbial ecology. The researchers’ identification of phage promoters with high expression efficiency yet low phage fitness cost reflects a deep integration of molecular virology and bioengineering principles. This delicate balance is critical to maintaining sufficient phage populations for sustained therapy while achieving therapeutic protein concentrations effective in vivo.

The in vivo experiments, emphasizing both molecular assays of enzyme activity and phenotypic outcomes such as weight reduction, supply compelling evidence for the translational potential of phage-mediated therapeutics. Murine models of ulcerative colitis and obesity provide analogs to human pathology, supporting the relevance of these findings to probable clinical scenarios.

It is worth noting that the resident E. coli strains targeted by T4 phage are nonpathogenic, mitigating concerns around pathogenicity or unintended exacerbation of disease through bacterial lysis products. This strategy exemplifies precision microbiome manipulation, differentiating harmful bacteria from beneficial ones and enabling targeted therapeutic interventions.

Moreover, the durability of protein production enabled by repeated cycles of phage infection and bacterial lysis suggests a sustained therapeutic presence without the need for repeated drug administration. This could revolutionize treatment paradigms for chronic diseases requiring continuous intervention, enhancing patient compliance and reducing systemic side effects.

Despite these promising advances, challenges remain in scalability, manufacturing, and regulatory approval of engineered phages for human use. Careful evaluation of immune responses to phage components and heterologous proteins, potential horizontal gene transfer risks, and long-term ecological impacts on gut microbiota are essential next steps.

Overall, this pioneering work marks a significant milestone in synthetic biology-driven therapeutics, demonstrating that virulent bacteriophages can serve as bespoke delivery vehicles for protein drugs directly within the gut. By integrating precise genetic engineering, phage biology, and understanding of host-microbe interactions, the study lays foundational groundwork for future phage-based oral biologics with transformative clinical potential.

Subject of Research: Engineering virulent bacteriophage T4 to deliver therapeutic proteins by infecting resident gut Escherichia coli to treat inflammatory diseases and metabolic disorders.

Article Title: Sustained in situ protein production and release in the mammalian gut by an engineered bacteriophage.

Article References:
Baker, Z.R., Zhang, Y., Zhang, H. et al. Sustained in situ protein production and release in the mammalian gut by an engineered bacteriophage. Nat Biotechnol (2025). https://doi.org/10.1038/s41587-025-02570-7

Image Credits: AI Generated

Tags: bacteriophage T4 engineered applicationsbiologic drug stability in acidic environmentscompetition with commensal gut bacteriaengineered bacteriophages for protein deliverygastrointestinal tract challenges in drug deliveryinnovative drug delivery systemslytic cycle of virulent phagesoral delivery methods for biologicsovercoming gastrointestinal drug delivery challengesphage therapy for biologicstherapeutic protein synthesis in guttherapeutic proteins release in gut microbiome