The Raffatellu Lab’s primary research focus is to understand the complex interplays between gut pathogens, mucosal immunity, and the gut microbiota, with the long-term goal of discovering novel and effective therapeutic targets for controlling infection. Our studies generally focus on the host response to gut mucosal pathogens such as Salmonella enterica, and we aim to decipher how the mucosal response to infection is orchestrated, including which components are beneficial to the host and which are evaded or exploited by pathogens to cause disease. Indeed, components of the immune response often constitute double-edged swords: on one edge, they are necessary to contain an infection to the mucosa; on the other edge, they can be leveraged by pathogens to outcompete the microbiota and to colonize the host. In order to unravel these complex interactions, we use a multidisciplinary research approach at the interface between microbiology and immunology, and we collaborate with many experts in related fields.

Below are synopses of some of our current projects.

Nutritional immunity during colitis
Mucosal surfaces are often the first interface between pathogenic microorganisms, the host, and the commensal microbiota. Among the most complex of these environments is the gut mucosa, where trillions of bacteria (the commensal microbiota) coexist with the host in a mutually beneficial equilibrium. Infection with enteric pathogens like Salmonella enterica serovar Typhimurium (STm) disrupts this equilibrium by causing intestinal inflammation, a host response that suppresses the growth of the commensal microbiota and favors the growth of STm by multiple mechanisms. Part of this response includes the upregulation of antimicrobial proteins that inhibit bacterial growth by limiting the availability of essential nutrients (including metal ions), a process that is termed “nutritional immunity”. A main focus of our lab is to investigate the mechanisms by which STm evades nutritional immunity and acquires metal ions in the inflamed gut, thus allowing the pathogen to successfully compete with the microbiota for these essential nutrients. We have discovered that Salmonella is able to acquire iron, zinc, and manganese in the gut by overcoming and evading metal sequestration mediated by host antimicrobial proteins lipocalin-2 and calprotectin, which in turn promotes the pathogen’s growth. Our research in this area has identified important virulence factors and potential therapeutic approaches for targeting Salmonella and other enteric pathogens.

Beneficial microbes: mechanisms of microbial competition
While investigating the mechanisms by which Salmonella evades nutritional immunity, we also sought to identify members of the gut microbiota that compete with pathogens for the same nutrients, and thus might be leveraged for preventing or controlling infection. We have discovered that a probiotic bacterium (Escherichia coli Nissle 1917) efficiently acquires iron and zinc in the inflamed gut, and effectively outcompetes Salmonella and other pathogenic organisms (e.g., adherent-invasive E. coli, AIEC). We discovered that microcins, which are narrow-spectrum antimicrobial peptides produced by E. coli Nissle, exert antimicrobial activity against these pathogens in the inflamed gut when iron availability is limited by nutritional immunity. We are now investigating the mechanisms of action of various microcins, and the extent of their activity against the gut microbiota. In collaboration with Dr. Elizabeth Nolan and her team at the MIT, we are also developing new strategies inspired by microbial competition for iron, in an effort to more specifically target enteric pathogens without broadly affecting the gut microbiota. In one project, we have developed a novel immunization strategy to induce an antibody response to a subset of bacterial siderophores (molecules used for metal acquisition), from which we are generating monoclonal antibodies. The Nolan Lab also conjugates siderophores to antibiotics, and we are planning to investigate these molecules’ ability to more selectively target Gram-negative pathogens in the host.

Mucosal Immunity during bacterial infection and colitis
Another goal of our research is to elucidate the role of bacterial virulence factors and host defenses during Salmonella’s interactions with the host. Many bacterial infections originate at mucosal surfaces such as the gut. STm and other non-typhoidal Salmonella serovars are among the leading causes of bacterial gastroenteritis, with infection resulting in a localized disease characterized by intestinal inflammation and a massive neutrophil influx to the intestinal mucosa. However, in patients with either primary or secondary immune deficiency, including the Acquired Immune Deficiency Syndrome (AIDS), STm may cause a life-threatening bacteremia. We discovered that STm induces a strong type-17 response in the gut mucosa, with production of IL-17A, IL-17F, and IL-22 by a variety of gut lymphocytes, which together orchestrate processes that recruit massive numbers of neutrophils. In addition to the CXC chemokines that are known to recruit neutrophils, we have recently discovered that neutrophil recruitment to the gut is also dependent on another mucosal chemokine: CCL28. Neutrophils isolated from the gut mucosa express the CCL28 receptors CCR3 and CCR10, and neutrophils stimulated with CCL28 exhibit enhanced antimicrobial activity against STm. On this front, we continue to investigate the role of CCL28 in mucosal immunity and neutrophil function.