Polysaccharide utilization and antimicrobial resistance in abundant GUT bacteria

The National Institute of General Medical Sciences awarded $434,169 to The Research Foundation for the State University of New York on March 1, 2026, under the Biomedical Research and Research Training program (CFDA 93.859) to support research on polysaccharide utilization and antimicrobial resistance in gut bacteria.

The Huang Lab will generate a genetic atlas of pathways among Bacteroidales bacteria important for polysaccharide utilization and tolerance to antibiotics, human-targeted drugs, and bile acids. The research applies high-throughput functional genomics and reductionist approaches to map how gut-abundant anaerobes access nutrients and tolerate antimicrobials, with findings intended to support development of strategies for harnessing the gut microbiota to promote health. The lab will interrogate gene functions of diverse Bacteroidales using a functional genomics platform that performs high-throughput fitness screens of DNA barcoded overexpression libraries to assay genes from multiple isolates and metagenomes in parallel.

Work is performed in Buffalo, New York, with performance running through February 28, 2031. The Research Foundation for the State University of New York, doing business as Sponsored Projects Services, serves as the fiscal agent administering the award on behalf of the State University of New York system.

Abstract

The trillions of microbes residing in the human GUT play critical roles in health and diseases. One critical function of the GUT microbiota is to provide colonization resistance to prevent pathogenic invasion and growth. Ingested and host-synthesized nutrients and antimicrobials are two major selective forces that shape and perturb the GUT microbiota composition. Despite the large amount of sequencing and -omics data from GUT microbiome research, the genetic basis for how GUT microbes respond to these dynamic factors remains largely uncharacterized. The high diversity of GUT microbes and the intricate network of microbe-microbe and host-microbe interactions make IT challenging to identify the underlying causative mechanisms. The huang lab seeks to advance our mechanistic understanding of key microbiota functions by applying cutting-edge, high-throughput genetics and reductionist approaches. This research plan will generate an atlas of pathways encoded among bacteroidales that are important for polysaccharide utilization and tolerance to antibiotics, human target drugs, and bile acids. By mapping the genetic network of how these GUT- abundant anaerobes access nutrients and tolerate antimicrobials, our findings will help to support the development of strategies for harnessing the GUT microbiota to promote health. We focus on bacteroidales because they are highly abundant in the healthy GUT and occupy the ecological niche of primary degraders of dietary fibers and host-derived glycans. We will interrogate gene functions of diverse bacteroidales by leveraging a functional genomics platform we previously established. This platform enables US to perform high-throughput fitness screens of DNA barcoded overexpression libraries using bacteroidales as chassis to assay genes from multiple isolates and metagenomes in parallel. We will adapt our platform to study pathways involved in polysaccharide metabolism and resistance to antibiotics, non-antibiotic drugs, and bile acids. The resulting fitness data will provide experimental evidence for novel gene functions and phenotypes. We will apply approaches in biochemistry, genetics, and bioinformatics to mechanistically dissect pathways of interest and evaluate their distribution across populations. The proposed research will advance our molecular understanding of how an abundant clade of GUT bacteria respond to major selective forces in the GUT environment. The overarching vision of our research program is to advance our mechanistic knowledge of how microbes colonize, grow, and survive in the human GUT. A long-term goal is to use our mechanistic findings to develop strategies to manipulate microbiota composition and function for health benefits.