Curtis Huttenhower
Other Positions
Faculty Affiliate in the Department of Immunology and Infectious Diseases
Immunology and Infectious Diseases
Harvard T.H. Chan School of Public Health
Overview
Research
Dr. Huttenhower’s research focuses on computational biology at the intersection of microbial community function and human health. The human body carries some four pounds of microbes, primarily in the gut, and understanding their biomolecular functions, their influences on human hosts, and the metabolic and functional roles of microbial communities generally is one of the key areas of study enabled by high-throughput sequencing. First, computational methods are needed to advance functional metagenomics. How can we understand what a microbial community is doing, what small molecule metabolites or signaling mechanisms it’s employing, and how its function relates to its organismal composition? Second, our understanding of the human microbiome and its relationship with public health remains limited. Pathogens have been examined by centuries of microbiology and epidemiology, but we know relatively little about the transmission or heritability of the normal commensal microbiota, its carriage of pathogenic functionality, or its interaction with host immunity, environment, and genetics. Finally, more broadly, novel machine learning methodology is needed to leverage structured biological knowledge in high-dimensional genomic data analysis. The Huttenhower group works on a variety of computational methods for data mining in microbial communities, model organisms, pathogens, and the human genome.
In practice, this entails a combination of computational methods development for mining and integrating large multi’omic data collections, as well as biological analyses and laboratory experiments to link the microbiome in human populations to specific microbiological mechanisms. The lab has worked extensively with the NIH Human Microbiome Project to help develop the first comprehensive map of the healthy Western adult microbiome, and it currently co-leads one of the “HMP2” Centers for Characterizing the Gut Microbial Ecosystem in Inflammatory Bowel Disease. This is one of many open problems in understanding how human-associated microbial communities can be used as a means of diagnosis or therapeutic intervention on the continuum between health and disease.
B.S., 2000, Computer Science/Math/Chemistry
Rose-Hulman Inst. of Tech.
M.S., 2003, Computer Science
Carnegie Mellon University
Ph.D. , 2008, Computer Science
Princeton University
Bibliography
A metabolomics pipeline highlights microbial metabolism in bloodstream infections.
Cell. 2024 Jun 16. PMID: 38885650
Author Correction: Optimized model architectures for deep learning on genomic data.
Gündüz HA, Mreches R, Moosbauer J, Robertson G, To XY, Franzosa EA, Huttenhower C, Rezaei M, McHardy AC, Bischl B, Münch PC, Binder M.
Commun Biol. 2024 May 23. 7(1):625. PMID: 38783006
Gut Microbiome Multi-Omics and Cognitive Function in the Hispanic Community Health Study/Study of Latinos- Investigation of Neurocognitive Aging.
Palacios N, Gordon S, Wang T, Burk R, Qi Q, Huttenhower C, Gonzalez HM, Knight R, De Carli C, Daviglus M, Lamar M, Telavera G, Tarraf W, Kosciolek T, Cai J, Kaplan RC.
medRxiv. 2024 May 17. PMID: 38798527
Appendectomy and Long-term Colorectal Cancer Incidence, Overall and by Tumor Fusobacterium nucleatum Status.
Kawamura H, Ugai T, Takashima Y, Okadome K, Shimizu T, Mima K, Akimoto N, Haruki K, Arima K, Zhao M, Väyrynen JP, Wu K, Zhang X, Ng K, Nowak JA, Meyerhardt JA, Giovannucci EL, Giannakis M, Chan AT, Huttenhower C, Garrett WS, Song M, Ogino S.
Ann Surg. 2024 May 06. PMID: 38708875
Elevated type-17 cytokines are present in axial spondyloarthritis stool.
Discov Immunol. 2024. 3(1):kyae005. PMID: 38966778
Optimized model architectures for deep learning on genomic data.
Gündüz HA, Mreches R, Moosbauer J, Robertson G, To XY, Franzosa EA, Huttenhower C, Rezaei M, McHardy AC, Bischl B, Münch PC, Binder M.
Commun Biol. 2024 Apr 30. 7(1):516. PMID: 38693292
Gut microbiome composition and metabolic activity in women with diverticulitis.
Ma W, Wang Y, Nguyen LH, Mehta RS, Ha J, Bhosle A, Mclver LJ, Song M, Clish CB, Strate LL, Huttenhower C, Chan AT.
Nat Commun. 2024 Apr 29. 15(1):3612. PMID: 38684664
Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria.
Li C, Stražar M, Mohamed AMT, Pacheco JA, Walker RL, Lebar T, Zhao S, Lockart J, Dame A, Thurimella K, Jeanfavre S, Brown EM, Ang QY, Berdy B, Sergio D, Invernizzi R, Tinoco A, Pishchany G, Vasan RS, Balskus E, Huttenhower C, Vlamakis H, Clish C, Shaw SY, Plichta DR, Xavier RJ.
Cell. 2024 Apr 11. 187(8):1834-1852.e19. PMID: 38569543
Altered Microbial Transcription in Long-term Proton Pump Inhibitor Use: Findings From a United States Cohort Study.
Gastroenterology. 2024 Jul. 167(2):405-408.e3. PMID: 38521094
News
Study links gut microbiome changes to increased risk of type 2 diabetes
Brigham, Broad, and Harvard Chan School researchers found that specific species and strains of bacteria were linked to changes in the functioning of the gut microbiome and a person's risk of type 2 diabetes.
![](https://www.hsph.harvard.edu/wp-content/uploads/sites/21/2024/06/iStock-1951948296.png)
Symposium explores microbiome’s roles in cancer
At the 6th annual symposium of the Harvard Chan Microbiome in Public Health Center, experts from around the world discussed the many ways that the microbiome contributes to the development and treatment of cancer.
![](https://www.hsph.harvard.edu/wp-content/uploads/sites/21/2024/05/Emily_Vogtmann_microbiome_1200x800.jpg)
Gut microbiome of pets reveals insights for human health
Curtis Huttenhower studies the role that the microbiome plays in health and disease, most often focusing on the human gut—but recently his research has expanded into pets, including dogs and cats.
![](https://www.hsph.harvard.edu/wp-content/uploads/sites/21/2023/06/Curtis_Huttenhower_Big_3.jpg)
Off the Cuff: Curtis Huttenhower
Curtis Huttenhower studies microbial communities starting at the population level. He hopes that by understanding how the microbiome affects a wide range of systems in the body, researchers will ultimately be able to target it to improve health…
New findings from Human Microbiome Project reveal how microbiome is disrupted during inflammatory bowel disease
Study finds chemical and molecular events that disrupt the microbiome and trigger immune responses during flare-ups of inflammatory bowel diseases.
![](https://www.hsph.harvard.edu/wp-content/uploads/sites/21/2019/05/MicrobiomeArt.jpg)