Integrated molecular approaches for fermented food microbiome research.
Walsh AM, Leech J, Huttenhower C, Delhomme-Nguyen H, Crispie F, Chervaux C, Cotter PD.
FEMS Microbiol Rev. 2023 03 10. 47(2). PMID: 36725208
Faculty Affiliate in the Department of Immunology and Infectious Diseases
Immunology and Infectious Diseases
Harvard T.H. Chan School of Public Health
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
Walsh AM, Leech J, Huttenhower C, Delhomme-Nguyen H, Crispie F, Chervaux C, Cotter PD.
FEMS Microbiol Rev. 2023 03 10. 47(2). PMID: 36725208
Mehta RS, Mayers JR, Zhang Y, Bhosle A, Glasser NR, Nguyen LH, Ma W, Bae S, Branck T, Song K, Sebastian L, Pacheco JA, Seo HS, Clish C, Dhe-Paganon S, Ananthakrishnan AN, Franzosa EA, Balskus EP, Chan AT, Huttenhower C.
Nat Med. 2023 Mar. 29(3):700-709. PMID: 36823301
Blanco-Míguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN, Zolfo M, Manghi P, Dubois L, Huang KD, Thomas AM, Nickols WA, Piccinno G, Piperni E, Puncochár M, Valles-Colomer M, Tett A, Giordano F, Davies R, Wolf J, Berry SE, Spector TD, Franzosa EA, Pasolli E, Asnicar F, Huttenhower C, Segata N.
Nat Biotechnol. 2023 Feb 23. PMID: 36823356
Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C, Konnikova L, Lebeer S, Macpherson AJ, Massey RC, McHardy AC, Koren O, Lawley TD, Ley RE, O'Mahony L, O'Toole PW, Pamer EG, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda DM, Smith GCS, Sokol H, Spector TD, Surette MG, Tannock GW, Walker AW, Yassour M, Walter J.
Nature. 2023 01. 613(7945):639-649. PMID: 36697862
Oyarzun JP, Kuntz TM, Stussi Y, Karaman OT, Vranos S, Callaghan BL, Huttenhower C, LeDoux JE, Phelps EA.
PNAS Nexus. 2022 Nov. 1(5):pgac271. PMID: 36712344
Zebrowska M, Strohmaier S, Westgarth C, Huttenhower C, Erber AC, Haghayegh S, Eliassen AH, Huang T, Laden F, Hart JE, Rosner B, Kawachi I, Chavarro JE, Okereke OI, Schernhammer ES.
J Affect Disord. 2023 02 15. 323:554-561. PMID: 36464093
Thompson KN, Oulhote Y, Weihe P, Wilkinson JE, Ma S, Zhong H, Li J, Kristiansen K, Huttenhower C, Grandjean P.
Environ Sci Technol. 2022 12 06. 56(23):16985-16995. PMID: 36394280
VanEvery H, Franzosa EA, Nguyen LH, Huttenhower C.
Nat Rev Genet. 2023 02. 24(2):109-124. PMID: 36198908
Wang Y, Wang K, Du M, Khandpur N, Rossato SL, Lo CH, VanEvery H, Kim DY, Zhang FF, Chavarro JE, Sun Q, Huttenhower C, Song M, Nguyen LH, Chan AT.
BMJ. 2022 10 05. 379:e071767. PMID: 36198411
Ma S, Shungin D, Mallick H, Schirmer M, Nguyen LH, Kolde R, Franzosa E, Vlamakis H, Xavier R, Huttenhower C.
Genome Biol. 2022 10 03. 23(1):208. PMID: 36192803
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…
For immediate release: May 29, 2019 Boston, MA – A new study led by researchers from Harvard T.H. Chan School of Public Health and the Broad Institute of MIT and Harvard is the first to have observed the complex…
May 24, 2019 – The microbiome—the collection of trillions of microorganisms throughout the body that plays an important role in numerous diseases—represents a promising frontier in the world of public health. Although it’s a relatively new field of…
In the coming decades, clarifying the many roles of the microbiome will dramatically reshape medicine and public health.
Scientists know that the gut microbiome is closely linked to human health, but little has been known about the roles of specific microorganisms. Now researchers from Harvard T.H. Chan School of Public Health, the Broad Institute of MIT…