Discovering how microbiome species metabolize heme and distribute iron - Project Summary Little is known about how beneficial bacteria in the digestive tract transform and use the host’s dietary iron, or how this impacts host iron uptake and health. Closing this knowledge gap is biomedically critical. On the one hand, iron-deficiency anemia is the most prevalent nutritional disorder worldwide, shared by nearly a third of the human population. On the other, unmetabolized iron in the form of heme, which is abundant in red meat diets, has been directly associated with gastrointestinal (GI) disorders ranging from inflammation to colon cancer. The long-term goal of this work is to understand how commensal bacteria commonly found in the healthy mammalian gut metabolize heme in the anaerobic, GI-tract ecosystem. The proposed work focuses our group’s knowledge and infrastructure – accrued over >15 years studying heme/iron biochemistry at the level of the catalyst, cell, and ecosystem – on this ambitious long-term goal, which we have divided into two overlapping parts. First, we will examine how common gut microbes metabolize heme. The most abundant members of the gut microbiome (from Bacteroidetes and Firmicutes phyla) are obligate anaerobes. They are also heme auxotrophs: species that require heme but lack the means to biosynthesize it. We showed that the heme utilization (hmu) operon provides the first and only characterized mechanism for breaking down heme in the anaerobic gastrointestinal (GI) tract, yielding free Fe2+ and a toxic pro-oxidant (protoporphyrin IX [PPIX]), as the initial products. We hypothesize that, by consuming heme, the hmu pathway could protect against heme-related pathologies. We will describe the structure, function, regulation, molecular interactions, and metabolic end products of the novel hmu pathway, using Bacteroides thetaiotaomicron as a model species. Members of its parent phylum (Bacteroidetes) are the only gut species with complete hmu operons, suggesting they play a commanding role in the gut’s heme metabolism. As our second objective, we will define how gut bacterial species work as a community and with the host to metabolize heme iron. We will address this objective using B. thetaiotaomicron and three additional widespread, non-pathogenic, strains that span known heme usage strategies in gut species. These strains form a foundational toolkit for studying iron metabolism in co-cultivation experiments, using chemically defined media in liquid and spatially organized biofilm formats. In parallel, we will examine the roles of the same species interrelationships, the hmu operon, and chemically defined dietary iron in our validated, gnotobiotic mouse model. Understanding heme metabolism by commensal bacteria serves the long-term biomedical goal of manipulating the microbiome to facilitate host metabolism of iron, thereby remediating diseases associated with iron deficiency (anemia) or excess (infection, dysbiosis, colitis, inflammation, colon cancer).
