A computational method to dissect colonization resistance of the gut microbiota against pathogens.

ABSTRACT: The mammalian gut microbiome protects the host through colonization resistance (CR) against the incursion of exogenous and often harmful microorganisms, but identifying the exact microbes responsible for the gut microbiota-mediated CR against a particular pathogen remains a challenge. To address this limitation, we developed a computational method: generalized microbe-phenotype triangulation (GMPT). We first systematically validated GMPT using a classical population dynamics model in community ecology and demonstrated its superiority over baseline methods. We then tested GMPT on simulated data generated from the ecological network inferred from a real community (GnotoComplex microflora) and real microbiome data on two mouse studies on Clostridioides difficile infection. We demonstrated GMP

SUBMITTER: Ke S 

PROVIDER: S-EPMC10545914 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature