Computational Method to Identify Bacterial Genes and Strains for Enhanced GI Tract Colonization

This technology is a computational discovery platform that pinpoints bacterial genes and gene combinations driving colonization of the mammalian gastrointestinal (GI) tract. It enables the design of engineered strains and gene reagents to advance microbiome research and therapeutic development.

Unmet Need: Tools for Precise Modulation of Gut Colonization

The genetic basis of bacterial colonization in the GI tract remains poorly defined, limiting efforts to predictably control colonization efficiency. Without precise tools, researchers cannot easily isolate or modulate the genes responsible for colonization, slowing the translation of microbiome discoveries into targeted interventions and therapies. These tools are essential for translating discoveries into targeted interventions and for developing therapeutic strategies that require precise control of bacterial colonization in the mammalian GI tract.

The Technology: Computational Discovery of Bacterial Genes for Improved Gut Colonization

This method identifies genes and gene combinations that influence bacterial colonization efficiency in the mammalian gastrointestinal (GI) tract. The approach allows for the selection of candidate genetic factors that can be incorporated into plasmid-based reagents or engineered bacterial strains, which can overexpress or carry the identified genes. These tools enable more precise studies and controlled modulation of bacterial colonization dynamics, offering a foundation for future therapeutic applications.

This technology has been validated with a colonizing E. coli strain in the mouse GI tract.

Applications:

• Research tools to analyze bacterial colonization mechanisms
• Therapeutic development of tools modulating the gut microbiome
• Genetic reagents and strains for investigating the microbiome
• Screening platforms to identify bacterial genes and colonization pathways
• Engineered bacterial strains for use as model systems for the microbiome

Advantages:

• Identifies bacterial genes and gene combinations driving colonization with high precision
• Supports research tools and translational therapeutic strategies
• Scalable across multiple bacterial species, genetic strains, and host models
• Provides reproducible modulation of colonization efficiency for diverse bacteria

Lead Inventor:

Saeed Tavazoie, Ph.D.

Patent Information:

Patent Pending

Related Publications:

• Liu M, Blattman SB, Takahashi M, Mandayam N, Jiang W, Oikonomou P, Tavazoie SF, Tavazoie S. “Conserved genetic basis for microbial colonization of the gut.” Cell. 2025 May 15; 188(10): 2823-2824.

Tech Ventures Reference:

• IR CU24221

• Licensing Contact: Joan Martinez