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Photo of Matthew Henke

Matthew Henke

Assistant Professor, Pharmaceutical Sciences


Office Phone:

(312) 996-3371 (work)

About Heading link

I am a chemist by training, with a special focus on microbial natural products and mass spectrometry. I have become increasingly fascinated by how our own microbial symbionts shape so many aspects of our biology. I’m amazed by how little chemical understanding there is in our understanding of the human microbiome. My lab’s primary goal is to change that.

Research Interests:
I am interested in how the microbes that colonize our bodies influence our health and in many cases drive our disease outcomes. The literature is full of examples of specific microbial species linked to host phenotypes, such as altering susceptibility to pathogen infection, modulating immune cell levels or responses, effecting visceral fat uptake, inducing certain cancers, and even rendering cancer treatments ineffective. Many groups are pursuing microbe-based treatments (e..g, probiotics and fecal microbiota transplants), despite significant unresolved barriers to getting such therapies to the clinic, including FDA regulations, safety concerns, difficulties with formulation and product stability, person-to-person variability to microbial tolerance, colonization efficiencies and intended response.

The Henke Lab takes a chemical-first approach 1) to gain molecular and mechanistic understanding behind microbiome associations to health and disease and 2) to develop chemical tools that can be used to re-engineer host phenotypes or microbial community structure.
We are primarily interested in three area of research:
1) Cataloguing the functional chemical dark matter present in the human metabolome.
2) Exploring how microbial competition manifests in the gut and how this effects human health.
3) Identifying microbial molecular effectors driving human immune alterations.

Teaching and Supervision Heading link

Pharmacog Research Techniques (PSCI 520), 8/21/2023 – 12/1/2023
Seminar in Med Chem (MDCH 595), 8/21/2023 – 12/1/2023
Departmental Seminar (BPS 595), 8/21/2023 – 12/1/2023
PSCI Ph.D. Thesis Research (PSCI 599), 8/21/2023 – 12/1/2023
Undergrad Res Pharm Sci (PSCI 380), 1/9/2023 – 4/28/2023
PSCI Ph.D. Thesis Research (PSCI 599), 1/9/2023 – 4/28/2023
PSCI Ph.D. Thesis Research (PSCI 599), 8/22/2022 – 12/2/2022

Selected Grants

Marine sponge depsipeptides to minimize antibiotic collateral damage, National Institutes of Health (National Institute of Allergy and Infectious Diseases)., 5/19/2023 - 4/30/2025, Obligated Amount: $199875; Anticipated Amount: $439725

Selected Publications

Raherisoanjato, Jessia, Henke, Matthew T. (2023). Multi-arming ourselves against drug-resistant bacteria. Cell Host & Microbe, 31, (7), 1075-1076. doi:10.1016/j.chom.2023.06.011.

Vemulapalli, Vidyasiri, Donovan, Katherine A, Seegar, Tom CM, Rogers, Julia M, Bae, Munhyung, Lumpkin, Ryan J, Cao, Ruili, Henke, Matthew T, Ray, Soumya S, Fischer, Eric S, Cuny, Gregory D, Blacklow, Stephen C. (2021). Targeted Degradation of the Oncogenic Phosphatase SHP2. Biochemistry, 60, (34), 2593-2609. doi:10.1021/acs.biochem.1c00377.

Henke, Matthew T, Brown, Eric M, Cassilly, Chelsi D, Vlamakis, Hera, Xavier, Ramnik J, Clardy, Jon. (2021). Capsular polysaccharide correlates with immune response to the human gut microbe Ruminococcus gnavus. Proceedings of the National Academy of Sciences of the United States of America, 118, (20), e2007595118. doi:10.1073/pnas.2007595118.

Chaudhari, Snehal N, Harris, David A, Aliakbarian, Hassan, Luo, James N, Henke, Matthew T, Subramaniam, Renuka, Vernon, Ashley H, Tavakkoli, Ali, Sheu, Eric G, Devlin, A Sloan. (2021). Bariatric surgery reveals a gut-restricted TGR5 agonist with anti-diabetic effects. Nature Chemical Biology, 17, (1), 20-29. doi:10.1038/s41589-020-0604-z.

Brugger, Silvio D, Eslami, Sara M, Pettigrew, Melinda M, Escapa, Isabel F, Henke, Matthew T, Kong, Yong, Lemon, Katherine P. (2020). Dolosigranulum pigrum Cooperation and Competition in Human Nasal Microbiota. mSphere, 5, (5), e00852-e00820. doi:10.1128/msphere.00852-20.

Fukuda, Taise TH, Cassilly, Chelsi D, Gerdt, Joseph P, Henke, Matthew T, Helfrich, Eric JN, Mevers, Emily. (2020). Research Tales from the Clardy Laboratory: Function-Driven Natural Product Discovery. Journal of Natural Products, 83, (3), 744-755. doi:10.1021/acs.jnatprod.9b01086.

Henke, Matthew T, Clardy, Jon. (2019). Molecular messages in human microbiota. Science, 366, (6471), 1309-1310. doi:10.1126/science.aaz4164.

Mevers, Emily, Saurí, Josep, Helfrich, Eric JN, Henke, Matthew, Barns, Kenneth J, Bugni, Tim S, Andes, David, Currie, Cameron R, Clardy, Jon. (2019). Pyonitrins A–D: Chimeric Natural Products Produced by Pseudomonas protegens. Journal of the American Chemical Society, 141, (43), 17098-17101. doi:10.1021/jacs.9b09739.

Henke, Matthew T, Kenny, Douglas J, Cassilly, Chelsi D, Vlamakis, Hera, Xavier, Ramnik J, Clardy, Jon. (2019). Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn’s disease, produces an inflammatory polysaccharide. Proceedings of the National Academy of Sciences of the United States of America, 116, (26), 12672-12677. doi:10.1073/pnas.1904099116.