Identifying gene-level host/bacterial interactions that regulate intestinal inflammation

The National Institute of Diabetes and Digestive and Kidney Diseases awarded the University of Pittsburgh $698,501 on September 1, 2026, under the Diabetes, Digestive, and Kidney Diseases Extramural Research program (CFDA 93.847) to identify gene-level interactions between host immunity and the intestinal microbiota that regulate inflammation in inflammatory bowel disease.

The funded research combines microbiota analysis tools, host single-cell RNA sequencing, and machine learning methods to identify conserved gene networks that define host–microbiota interactions during intestinal inflammation. The work develops and applies a microbiota flow cytometry method called MicFly to achieve single-cell resolution of bacterial taxa, including targeted transcriptomics on individual taxa sorted prior to RNA sequencing (MicFly-seq). The recipient will study gnotobiotic mice with defined bacterial consortia as they respond to five acute intestinal inflammation models at defined timepoints to map the core set of genes induced within the microbiome during inflammatory events and their interaction with immune cells.

Work is performed at the University of Pittsburgh, Pittsburgh, Pennsylvania. The period of performance runs from September 1, 2026, through June 30, 2031. The award is classified as a Project Grant, an assistance type supporting extramural basic and clinical biomedical research that improves understanding of disease mechanisms and leads to improved prevention, diagnosis, and treatment of diabetes, digestive, and kidney diseases.

Abstract

Inflammatory bowel disease (IBD) causes chronic pain and suffering to millions of americans and currently there is no cure. While the underlying mechanisms of IBD remain unknown, the interaction between the microbiota and the intestinal immune response is critical. The intestinal immune response has evolved to tolerate colonization with the microbiota but how this relationship deteriorates during IBD is not clear. All intestinal inflammatory diseases and infections induce a similar shift the in the microbiota, characterized by a drop in microbiota diversity driven by an increase in facultative anaerobes, such as enterobacteriaceae. Inflammation-induced shifts in the intestinal microbiota are consistent across host species, implying that intestinal bacteria have developed mechanisms to directly modulate immune cells and either promote or suppress inflammation, depending upon whether the bacteria are benefitted or disadvantaged. Our hypothesis is that there is a core set of genes induced within the microbiome during inflammatory events that interact with the cells of the immune system to either drive or regulate intestinal inflammation. Here we propose to combine novel microbiota analysis tools, host single cell rnaseq and machine learning methods to identify conserved networks that define the interaction between host immunity and the microbiota during inflammation. To analyze the microbiota at single cell scale, we developed (microbiota flow cytometry; MICFLY) a method that provides accurate quantitative resolution of bacteria at all taxonomic levels. MICFLY can be used to perform targeted transcriptomics on individual taxa within a diverse microbiota by sorting bacteria prior to rnaseq (MICFLY- SEQ). We propose to study gnotobiotic mice with a defined consortium of bacteria as they respond to five acute intestinal inflammation models. At defined timepoints of the inflammation models we will isolate each member of the bacterial consortia and measure their transcriptomes (MICFLY-SEQ). Taxon-specific transcriptomic data can then be coupled to concurrently collected host single cell rnaseq data using innovative machine learning analytic tools to identify bacterial/host gene interaction networks that are conserved across the inflammatory models. Identified bacterial networks will be confirmed in human samples from IBD and necrotizing enterocolitis patients. Identification of conserved mechanisms by which the microbiome drives intestinal inflammation has extraordinary promise to develop novel and universal microbiome-targeting drugs and add substantially to our knowledge of the microbiota and mucosal immunology. This project also will serve as an example of the power of our technology to measure the transcriptome of individual bacteria in a mixed population, catalyzing future host/microbiome research.