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Research Themes

The oral microbiota is emerging as an important driver of local and systemic inflammatory disease. Like microbial communities at other body sites, the oral microbiota comprises both commensals and pathogens (commensals with inflammatory potential that are also present in health). The balance between these taxa - and thus host susceptibility to disease - is strongly shaped by host-derived metabolites. These molecules can directly serve as nutrients for microbial growth, and depending on the host’s immune status, they can determine the outcome of polymicrobial interactions (for example, whether commensals outcompete pathogens or vice versa).


The long-term goal of the Apollo Lab is to translate host-derived metabolites into microbiota-directed therapies. To this end, we leverage an interdisciplinary approach involving bacterial genetics, genomics, animal models, immune profiling, and human samples. The disease that we primarily study is periodontitis, or inflammation of the tissues that support the teeth. This prevalent condition can result in tooth loss, and it also increases risk for a range of diseases in and outside the oral cavity, including oral cancer and heart infection. Projects in the lab fall under one of the two themes below.

Training commensals

Gym Equipments

In response to infection, the host can increase the availability of metabolites that nourish commensals. Once “trained” by inflammation-induced metabolites, commensals can in turn enhance host resistance to subsequent infection. While this phenomenon was first described in the gut, we hypothesize that it also occurs in response to inflammation at other barrier sites, such as periodontitis in the oral cavity. Current projects are focused on nitrate, a periodontitis-induced host metabolite that can  elicit oral commensals by acting as an electron acceptor. We are exploring whether host and/or dietary nitrate can mitigate periodontitis by promoting commensals over pathogens.

Targeting pathogens

Unchecked inflammation can generate metabolites that favor the outgrowth of pathogens. Preventing pathogens from exploiting such metabolites may represent a more targeted approach for treating microbiota-driven diseases, in contrast to antibiotics which also kill commensals. Current projects are focused on the microbiota-derived metabolite formate, the production of which we hypothesize is stimulated by inflammation-induced hypoxia. To exploit formate, pathogens require the micronutrient selenium. Based on this, we are exploring whether depleting selenium can mitigate periodontitis by targeting pathogen formate metabolism. We are also developing an interest in defining the metabolites that pathogens exploit in the setting of oral squamous cell carcinoma.

Image by Silvan Arnet

Selected Publications

Remembrance of infections past

Stacy A

Science  |  2022  |  PDF

Infection trains the host for microbiota-enhanced resistance to pathogens

Stacy A†, Andrade-Oliveira V, McCulloch JA, Hild B, Oh JH, Perez-Chaparro PJ, Sim CK, Lim AI, Link VM, Enamorado M, Trinchieri G, Segre JA, Rehermann B, Belkaid Y†

†Co-corresponding author

Cell  |  2021  |  PDF


Large-scale identification of pathogen essential genes during coinfection with sympatric and allopatric microbes


Lewin GR, Stacy A, Michie KL, Lamont RJ, Whiteley M


PNAS  |  2019  |  PDF


Defining genetic fitness determinants and creating genomic resources for an oral pathogen

Narayanan AM, Ramsey MM, Stacy A†, Whiteley M†  †Co-corresponding author


Applied and Environmental Microbiology  |  2017  |  PDF

Co-infecting microbes dramatically alter pathogen gene essentiality during polymicrobial infection


Ibberson CB, Stacy A, Fleming D, Dees JL, Rumbaugh K, Gilmore MS, Whiteley M


Nature Microbiology  |  2017  |  PDF

A commensal bacterium promotes virulence of an opportunistic pathogen via cross-respiration


Stacy A, Fleming D, Lamont RJ, Rumbaugh KP, Whiteley M


mBio  |  2016  |  PDF

Microbial community composition impacts pathogen iron availability during polymicrobial infection


Stacy A, Abraham N, Jorth P, Whiteley M

PLOS Pathogens  |  2016  |  PDF

The biogeography of polymicrobial infection

Stacy A, McNally L, Darch SE, Brown SP, Whiteley M

Nature Reviews Microbiology  |  2016  |  PDF


Bacterial fight-and-flight responses enhance virulence in a polymicrobial infection


Stacy A, Everett J, Jorth P, Trivedi U, Rumbaugh KP, Whiteley M


PNAS  |  2014  |  PDF


View complete list of publications

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