Development of genetic systems for the manipulation and targeted isolation of human GUT microbes

The National Institute of Allergy and Infectious Diseases awarded $433,125 to the Regents of the University of California at Riverside on July 20, 2026, under the Allergy and Infectious Diseases Research program (CFDA 93.855) to develop genetic systems for manipulation and targeted isolation of human gut microbes.

The funded research constructs novel shuttle vectors to enable genetic manipulation of cultured gut microbial species and aid in efficient isolation of slow-growing, recalcitrant species from complex communities. The work addresses a gap in currently available genetic tools for phenotypically important gut commensals. The project involves construction of species-specific vectors for gram-positive commensals using predicted native plasmids and drug resistance cassettes, and deployment of these vectors for targeted microbe enrichment from complex microbial mixtures. These genetic tools will support mechanistic studies of microbe-microbe and microbe-host interactions that drive health and disease outcomes.

Performance takes place in Riverside, California with a period of performance from award date through June 30, 2028. The award is classified as a Project Grant under the assistance type structure.

Abstract

The human GUT microbiota comprises large and diverse microbial communities, including bacteria, viruses, and eukaryotes, components of which have been discovered to significantly impact various host phenotypes, such as nutrition, immunity and inflammation, and infection outcomes. Culture-independent approaches such as 16S rrna and metagenomic studies have provided many insights into the microbiome's contributions to health and disease. However, the ability to isolate, culture, and genetically manipulate specific individual microbes is crucial for mechanistic understanding of the complex microbe-microbe and microbe-host interactions that drive microbe-dependent human health phenotypes. Currently, the catalog of cultured and genetically tractable GUT microbes is biased toward faster-growing, abundant, generalist species. Slow-growing, low-abundance, or microbes with specific nutritional needs are often underrepresented in culture collections despite their potentially important roles in host health. Moreover, even among cultured GUT microbes, genetic tools for manipulation and detailed study of their roles in health and disease are not available. We hypothesize that the construction of novel shuttle vectors will enable both the manipulation of available type strains of phenotypically important GUT microbes and aid in the efficient isolation of novel, recalcitrant species and strains from complex communities. To test our hypotheses, we will (aim i) construct species-specific vectors for a selection of gram-positive commensals that drive important host phenotypes using predicted native plasmids and drug resistance cassettes. We will also (aim II) deploy these novel species-specific vectors for targeted microbe enrichment from complex microbial mixtures. These aims will generate needed genetic tools for key GUT microbial species, providing a blueprint for developing similar tools for other commensal GUT species and isolating microbes from complex environments like soil and wastewater.