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Curtis Huttenhower, Ph.D.

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Biography
Rose-Hulman Inst. of Tech.B.S. 2000Computer Science/Math/Chemistry
Carnegie Mellon UniversityM.S.2003Computer Science
Princeton UniversityPh.D. 2008Computer Science

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.

Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. T32GM135117 (LIN, XIHONG) Jul 1, 2020 - Jun 30, 2025
    NIH
    Interdisciplinary training: Statistical Genetics/Genomics and Computational Biology
    Role: Co-Principal Investigator
  2. R24DK110499 (HUTTENHOWER, CURTIS) Sep 20, 2017 - Jun 30, 2022
    NIH
    A comprehensive platform for novel therapy development from the microbiome
    Role: Principal Investigator
  3. R01CA202704 (CHAN, ANDREW T) Mar 1, 2016 - Feb 28, 2021
    NIH
    Dietary sulfur, the gut microbiome, and colorectal cancer
    Role: Co-Principal Investigator
  4. R21AI112991 (HUTTENHOWER, CURTIS) Aug 10, 2015 - Jul 31, 2018
    NIH
    Staphylococcus Aureus Carriage and the Nasal Microbiome
    Role: Principal Investigator
  5. U54DK102557 (XAVIER, RAMNIK J) Sep 6, 2013 - Aug 31, 2017
    NIH
    Characterizing the gut microbial ecosystem for diagnosis and therapy in IBD
    Role: Principal Investigator

Featured Content

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. 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. Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease. Nat Med. 2023 Feb 23. PMID: 36823301.
    Citations:    Fields:    
  2. 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. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat Biotechnol. 2023 Feb 23. PMID: 36823356.
    Citations: 2     Fields:    
  3. Walsh AM, Leech J, Huttenhower C, Delhomme-Nguyen H, Crispie F, Chervaux C, Cotter PD. "Integrated molecular approaches for fermented food microbiome research". FEMS Microbiol Rev. 2023 Feb 01. PMID: 36725208.
    Citations:    Fields:    
  4. 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. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature. 2023 01; 613(7945):639-649. PMID: 36697862.
    Citations:    Fields:    Translation:HumansAnimals
  5. Oyarzun JP, Kuntz TM, Stussi Y, Karaman OT, Vranos S, Callaghan BL, Huttenhower C, LeDoux JE, Phelps EA. Human threat learning is associated with gut microbiota composition. PNAS Nexus. 2022 Nov; 1(5):pgac271. PMID: 36712344; PMCID: PMC9802442.
    Citations:    
  6. 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. Relationship between pet ownership and risk of high depressive symptoms in adolescence and young adulthood. J Affect Disord. 2023 Feb 15; 323:554-561. PMID: 36464093; PMCID: PMC9839520.
    Citations:    Fields:    Translation:HumansAnimals
  7. Thompson KN, Oulhote Y, Weihe P, Wilkinson JE, Ma S, Zhong H, Li J, Kristiansen K, Huttenhower C, Grandjean P. Effects of Lifetime Exposures to Environmental Contaminants on the Adult Gut Microbiome. Environ Sci Technol. 2022 12 06; 56(23):16985-16995. PMID: 36394280.
    Citations:    Fields:    Translation:Humans
  8. 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. Maternal consumption of ultra-processed foods and subsequent risk of offspring overweight or obesity: results from three prospective cohort studies. BMJ. 2022 10 05; 379:e071767. PMID: 36198411.
    Citations:    Fields:    Translation:Humans
  9. VanEvery H, Franzosa EA, Nguyen LH, Huttenhower C. Microbiome epidemiology and association studies in human health. Nat Rev Genet. 2023 02; 24(2):109-124. PMID: 36198908.
    Citations:    Fields:    Translation:Humans
  10. Ma S, Shungin D, Mallick H, Schirmer M, Nguyen LH, Kolde R, Franzosa E, Vlamakis H, Xavier R, Huttenhower C. Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin. Genome Biol. 2022 10 03; 23(1):208. PMID: 36192803; PMCID: PMC9531436.
    Citations: 2     Fields:    Translation:Humans
  11. Bhosle A, Wang Y, Franzosa EA, Huttenhower C. Progress and opportunities in microbial community metabolomics. Curr Opin Microbiol. 2022 12; 70:102195. PMID: 36063685.
    Citations: 1     Fields:    
  12. Yao L, D'Agostino GD, Park J, Hang S, Adhikari AA, Zhang Y, Li W, Avila-Pacheco J, Bae S, Clish CB, Franzosa EA, Huttenhower C, Huh JR, Devlin AS. A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria. Nat Microbiol. 2022 09; 7(9):1404-1418. PMID: 35982310.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  13. Arima K, Zhong R, Ugai T, Zhao M, Haruki K, Akimoto N, Lau MC, Okadome K, Mehta RS, Väyrynen JP, Kishikawa J, Twombly TS, Shi S, Fujiyoshi K, Kosumi K, Ogata Y, Baba H, Wang F, Wu K, Song M, Zhang X, Fuchs CS, Sears CL, Willett WC, Giovannucci EL, Meyerhardt JA, Garrett WS, Huttenhower C, Chan AT, Nowak JA, Giannakis M, Ogino S. Western-Style Diet, pks Island-Carrying Escherichia coli, and Colorectal Cancer: Analyses From Two Large Prospective Cohort Studies. Gastroenterology. 2022 10; 163(4):862-874. PMID: 35760086; PMCID: PMC9509428.
    Citations:    Fields:    
  14. Ghazi AR, Sucipto K, Rahnavard A, Franzosa EA, McIver LJ, Lloyd-Price J, Schwager E, Weingart G, Moon YS, Morgan XC, Waldron L, Huttenhower C. High-sensitivity pattern discovery in large, paired multiomic datasets. Bioinformatics. 2022 06 24; 38(Suppl 1):i378-i385. PMID: 35758795; PMCID: PMC9235493.
    Citations:    Fields:    Translation:Cells
  15. Lai P, Nguyen L, Okin D, Drew D, Battista V, Jesudasen S, Kuntz T, Bhosle A, Thompson K, Reinicke T, Lo CH, Woo J, Caraballo A, Berra L, Vieira J, Huang CY, Adhikari UD, Kim M, Sui HY, Magicheva-Gupta M, McIver L, Goldberg M, Kwon D, Huttenhower C, Chan A. Metagenomic assessment of gut microbial communities and risk of severe COVID-19. Res Sq. 2022 Jun 07. PMID: 35677075; PMCID: PMC9176657.
    Citations: 1     
  16. Zhang Y, Bhosle A, Bae S, McIver LJ, Pishchany G, Accorsi EK, Thompson KN, Arze C, Wang Y, Subramanian A, Kearney SM, Pawluk A, Plichta DR, Rahnavard A, Shafquat A, Xavier RJ, Vlamakis H, Garrett WS, Krueger A, Huttenhower C, Franzosa EA. Discovery of bioactive microbial gene products in inflammatory bowel disease. Nature. 2022 06; 606(7915):754-760. PMID: 35614211; PMCID: PMC9913614.
    Citations:    Fields:    Translation:HumansCells
  17. Zhang S, Morgan X, Dogan B, Martin FP, Strickler S, Oka A, Herzog J, Liu B, Dowd SE, Huttenhower C, Pichaud M, Dogan EI, Satsangi J, Longman R, Yantiss R, Mueller LA, Scherl EJ, Sartor RB, Simpson KW. Mucosal metabolites fuel the growth and virulence of E. coli linked to Crohn's disease. JCI Insight. 2022 05 23; 7(10). PMID: 35413017; PMCID: PMC9220930.
    Citations:    Fields:    Translation:AnimalsCells
  18. Ghazi AR, Münch PC, Chen D, Jensen J, Huttenhower C. Strain Identification and Quantitative Analysis in Microbial Communities. J Mol Biol. 2022 08 15; 434(15):167582. PMID: 35398320.
    Citations:    Fields:    
  19. Li Y, Wang F, Li J, Ivey KL, Wilkinson JE, Wang DD, Li R, Liu G, Eliassen HA, Chan AT, Clish CB, Huttenhower C, Hu FB, Sun Q, Rimm EB. Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome. BMC Microbiol. 2022 03 29; 22(1):82. PMID: 35350985; PMCID: PMC8966171.
    Citations:    Fields:    Translation:Humans
  20. Mehta RS, Lochhead P, Wang Y, Ma W, Nguyen LH, Kochar B, Huttenhower C, Grodstein F, Chan AT. Association of midlife antibiotic use with subsequent cognitive function in women. PLoS One. 2022; 17(3):e0264649. PMID: 35320274; PMCID: PMC8942267.
    Citations:    Fields:    Translation:Humans
  21. Paik D, Yao L, Zhang Y, Bae S, D'Agostino GD, Zhang M, Kim E, Franzosa EA, Avila-Pacheco J, Bisanz JE, Rakowski CK, Vlamakis H, Xavier RJ, Turnbaugh PJ, Longman RS, Krout MR, Clish CB, Rastinejad F, Huttenhower C, Huh JR, Devlin AS. Human gut bacteria produce ??17-modulating bile acid metabolites. Nature. 2022 03; 603(7903):907-912. PMID: 35296854; PMCID: PMC9132548.
    Citations: 8     Fields:    Translation:HumansCells
  22. Orwoll ES, Parimi N, Wiedrick J, Lapidus J, Napoli N, Wilkinson JE, Huttenhower C, Langsetmo L, Kiel DP. Analysis of the Associations Between the Human Fecal Microbiome and Bone Density, Structure, and Strength: The Osteoporotic Fractures in Men (MrOS) Cohort. J Bone Miner Res. 2022 04; 37(4):597-607. PMID: 35119137; PMCID: PMC9605688.
    Citations: 1     Fields:    Translation:Humans
  23. Wang DD, Qi Q, Wang Z, Usyk M, Sotres-Alvarez D, Mattei J, Tamez M, Gellman MD, Daviglus M, Hu FB, Stampfer MJ, Huttenhower C, Knight R, Burk RD, Kaplan RC. The Gut Microbiome Modifies the Association Between a Mediterranean Diet and Diabetes in USA Hispanic/ Latino Population. J Clin Endocrinol Metab. 2022 02 17; 107(3):e924-e934. PMID: 34747479; PMCID: PMC8851916.
    Citations:    Fields:    Translation:Humans
  24. Park SY, Rao C, Coyte KZ, Kuziel GA, Zhang Y, Huang W, Franzosa EA, Weng JK, Huttenhower C, Rakoff-Nahoum S. Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite. Cell. 2022 02 03; 185(3):513-529.e21. PMID: 35120663; PMCID: PMC8896310.
    Citations: 3     Fields:    Translation:Cells
  25. McFarland AG, Kennedy NW, Mills CE, Tullman-Ercek D, Huttenhower C, Hartmann EM. Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper. Bioinformatics. 2022 01 12; 38(3):612-620. PMID: 34734968.
    Citations: 1     Fields:    
  26. Spencer CN, McQuade JL, Gopalakrishnan V, McCulloch JA, Vetizou M, Cogdill AP, Khan MAW, Zhang X, White MG, Peterson CB, Wong MC, Morad G, Rodgers T, Badger JH, Helmink BA, Andrews MC, Rodrigues RR, Morgun A, Kim YS, Roszik J, Hoffman KL, Zheng J, Zhou Y, Medik YB, Kahn LM, Johnson S, Hudgens CW, Wani K, Gaudreau PO, Harris AL, Jamal MA, Baruch EN, Perez-Guijarro E, Day CP, Merlino G, Pazdrak B, Lochmann BS, Szczepaniak-Sloane RA, Arora R, Anderson J, Zobniw CM, Posada E, Sirmans E, Simon J, Haydu LE, Burton EM, Wang L, Dang M, Clise-Dwyer K, Schneider S, Chapman T, Anang NAS, Duncan S, Toker J, Malke JC, Glitza IC, Amaria RN, Tawbi HA, Diab A, Wong MK, Patel SP, Woodman SE, Davies MA, Ross MI, Gershenwald JE, Lee JE, Hwu P, Jensen V, Samuels Y, Straussman R, Ajami NJ, Nelson KC, Nezi L, Petrosino JF, Futreal PA, Lazar AJ, Hu J, Jenq RR, Tetzlaff MT, Yan Y, Garrett WS, Huttenhower C, Sharma P, Watowich SS, Allison JP, Cohen L, Trinchieri G, Daniel CR, Wargo JA. Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response. Science. 2021 Dec 24; 374(6575):1632-1640. PMID: 34941392; PMCID: PMC8970537.
    Citations: 31     Fields:    Translation:HumansAnimalsCells
  27. Mirzayi C, Renson A, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, Beghini F, Bergstrom K, Bhatt A, Bisanz JE, Braun J, Bravo HC, Buck GA, Bushman F, Casero D, Clarke G, Collado MC, Cotter PD, Cryan JF, Demmer RT, Devkota S, Elinav E, Escobar JS, Fettweis J, Finn RD, Fodor AA, Forslund S, Franke A, Furlanello C, Gilbert J, Grice E, Haibe-Kains B, Handley S, Herd P, Holmes S, Jacobs JP, Karstens L, Knight R, Knights D, Koren O, Kwon DS, Langille M, Lindsay B, McGovern D, McHardy AC, McWeeney S, Mueller NT, Nezi L, Olm M, Palm N, Pasolli E, Raes J, Redinbo MR, Rühlemann M, Balfour Sartor R, Schloss PD, Schriml L, Segal E, Shardell M, Sharpton T, Smirnova E, Sokol H, Sonnenburg JL, Srinivasan S, Thingholm LB, Turnbaugh PJ, Upadhyay V, Walls RL, Wilmes P, Yamada T, Zeller G, Zhang M, Zhao N, Zhao L, Bao W, Culhane A, Devanarayan V, Dopazo J, Fan X, Fischer M, Jones W, Kusko R, Mason CE, Mercer TR, Sansone SA, Scherer A, Shi L, Thakkar S, Tong W, Wolfinger R, Hunter C, Segata N, Huttenhower C, Dowd JB, Jones HE, Waldron L. Reporting guidelines for human microbiome research: the STORMS checklist. Nat Med. 2021 11; 27(11):1885-1892. PMID: 34789871; PMCID: PMC9105086.
    Citations: 15     Fields:    Translation:Humans
  28. Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput Biol. 2021 11; 17(11):e1009442. PMID: 34784344; PMCID: PMC8714082.
    Citations: 80     Fields:    Translation:Humans
  29. Wang Y, Nguyen LH, Mehta RS, Song M, Huttenhower C, Chan AT. Association Between the Sulfur Microbial Diet and Risk of Colorectal Cancer. JAMA Netw Open. 2021 11 01; 4(11):e2134308. PMID: 34767023; PMCID: PMC8590167.
    Citations:    Fields:    Translation:HumansAnimalsCells
  30. Petrick JL, Wilkinson JE, Michaud DS, Cai Q, Gerlovin H, Signorello LB, Wolpin BM, Ruiz-Narváez EA, Long J, Yang Y, Johnson WE, Shu XO, Huttenhower C, Palmer JR. The oral microbiome in relation to pancreatic cancer risk in African Americans. Br J Cancer. 2022 02; 126(2):287-296. PMID: 34718358; PMCID: PMC8770575.
    Citations: 1     Fields:    Translation:Humans
  31. McGee JS, Huttenhower C. Of mice and men and women: Sexual dimorphism of the gut microbiome. Int J Womens Dermatol. 2021 Dec; 7(5Part A):533-538. PMID: