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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

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. 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 Mar 29; 22(1):82. PMID: 35350985.
    Citations:    Fields:    
  2. 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.
    Citations:    Fields:    
  3. 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 Mar; 603(7903):907-912. PMID: 35296854.
    Citations:    Fields:    
  4. 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.
    Citations:    Fields:    Translation:Humans
  5. 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 Feb 04. PMID: 35119137.
    Citations:    Fields:    
  6. 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.
    Citations:    Fields:    Translation:Cells
  7. 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.
    Citations: 10     Fields:    Translation:HumansAnimalsCells
  8. 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.
    Citations: 3     Fields:    Translation:Humans
  9. 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.
    Citations: 42     Fields:    Translation:Humans
  10. 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. 2021 Nov 04. PMID: 34734968.
    Citations:    Fields:    
  11. 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.
    Citations:    Fields:    Translation:HumansAnimalsCells
  12. 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.
    Citations: 1     Fields:    Translation:Humans
  13. 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: 35005176.
    Citations:    
  14. Ma S, Ren B, Mallick H, Moon YS, Schwager E, Maharjan S, Tickle TL, Lu Y, Carmody RN, Franzosa EA, Janson L, Huttenhower C. A statistical model for describing and simulating microbial community profiles. PLoS Comput Biol. 2021 09; 17(9):e1008913. PMID: 34516542.
    Citations: 2     Fields:    
  15. Li Y, Wang DD, Satija A, Ivey KL, Li J, Wilkinson JE, Li R, Baden M, Chan AT, Huttenhower C, Rimm EB, Hu FB, Sun Q. Plant-Based Diet Index and Metabolic Risk in Men: Exploring the Role of the Gut Microbiome. J Nutr. 2021 09 04; 151(9):2780-2789. PMID: 34114015.
    Citations:    Fields:    Translation:Humans
  16. Everett C, Li C, Wilkinson JE, Nguyen LH, McIver LJ, Ivey K, Izard J, Palacios N, Eliassen AH, Willett WC, Ascherio A, Sun Q, Tworoger SS, Chan AT, Garrett WS, Huttenhower C, Rimm EB, Song M. Publisher Correction: Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies. Nat Protoc. 2021 Sep; 16(9):4538. PMID: 33986535.
    Citations:    Fields:    
  17. Li W, Hang S, Fang Y, Bae S, Zhang Y, Zhang M, Wang G, McCurry MD, Bae M, Paik D, Franzosa EA, Rastinejad F, Huttenhower C, Yao L, Devlin AS, Huh JR. A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1. Cell Host Microbe. 2021 09 08; 29(9):1366-1377.e9. PMID: 34416161.
    Citations: 7     Fields:    Translation:HumansCells
  18. Sikavi DR, Nguyen LH, Haruki K, Ugai T, Ma W, Wang DD, Thompson KN, Yan Y, Branck T, Wilkinson JE, Akimoto N, Zhong R, Lau MC, Mima K, Kosumi K, Morikawa T, Rimm EB, Garrett WS, Izard J, Cao Y, Song M, Huttenhower C, Ogino S, Chan AT. The Sulfur Microbial Diet and Risk of Colorectal Cancer by Molecular Subtypes and Intratumoral Microbial Species in Adult Men. Clin Transl Gastroenterol. 2021 08 01; 12(8):e00338. PMID: 34333506.
    Citations:    Fields:    Translation:HumansCells
  19. Nguyen LH, Cao Y, Hur J, Mehta RS, Sikavi DR, Wang Y, Ma W, Wu K, Song M, Giovannucci EL, Rimm EB, Willett WC, Garrett WS, Izard J, Huttenhower C, Chan AT. The Sulfur Microbial Diet Is Associated With Increased Risk of Early-Onset Colorectal Cancer Precursors. Gastroenterology. 2021 11; 161(5):1423-1432.e4. PMID: 34273347.
    Citations: 3     Fields:    Translation:HumansCells
  20. Zhang Y, Thompson KN, Huttenhower C, Franzosa EA. Statistical approaches for differential expression analysis in metatranscriptomics. Bioinformatics. 2021 07 12; 37(Suppl_1):i34-i41. PMID: 34252963.
    Citations: 2     Fields:    
  21. Ma W, Nguyen LH, Song M, Wang DD, Franzosa EA, Cao Y, Joshi A, Drew DA, Mehta R, Ivey KL, Strate LL, Giovannucci EL, Izard J, Garrett W, Rimm EB, Huttenhower C, Chan AT. Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men. Genome Med. 2021 06 17; 13(1):102. PMID: 34140026.
    Citations: 2     Fields:    Translation:HumansPHPublic Health
  22. Zhang Y, Thompson KN, Branck T, Nguyen LH, Franzosa EA, Huttenhower C. Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling. Annu Rev Biomed Data Sci. 2021 07 20; 4:279-311. PMID: 34465175.
    Citations: 4     Fields:    Translation:HumansCells
  23. Wang V, Geybels MS, Jordahl KM, Gerke T, Hamid A, Penney KL, Markt SC, Freedman M, Pomerantz M, Lee GM, Rana H, Börnigen D, Rebbeck TR, Huttenhower C, Eeles RA, Stanford JL, Consortium P, Berndt SI, Claessens F, Sørensen KD, Park JY, Vega A, Usmani N, Mucci L, Sweeney CJ. A polymorphism in the promoter of FRAS1 is a candidate SNP associated with metastatic prostate cancer. Prostate. 2021 07; 81(10):683-693. PMID: 33956343.
    Citations: 1     Fields:    Translation:HumansCells
  24. Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, Segata N. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Elife. 2021 05 04; 10. PMID: 33944776.
    Citations: 54     Fields:    Translation:HumansCells
  25. Li J, Li Y, Ivey KL, Wang DD, Wilkinson JE, Franke A, Lee KH, Chan A, Huttenhower C, Hu FB, Rimm EB, Sun Q. Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men. Gut. 2022 Apr; 71(4):724-733. PMID: 33926968.
    Citations: 6     Fields:    
  26. Everett C, Li C, Wilkinson JE, Nguyen LH, McIver LJ, Ivey K, Izard J, Palacios N, Eliassen AH, Willett WC, Ascherio A, Sun Q, Tworoger SS, Chan AT, Garrett WS, Huttenhower C, Rimm EB, Song M. Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies. Nat Protoc. 2021 06; 16(6):2724-2731. PMID: 33883746.
    Citations:    Fields:    Translation:Humans
  27. Simon TG, Chan AT, Huttenhower C. Microbiome Biomarkers: One Step Closer in NAFLD Cirrhosis. Hepatology. 2021 05; 73(5):2063-2066. PMID: 33283299.
    Citations: 1     Fields:    Translation:Humans
  28. Wilkinson JE, Franzosa EA, Everett C, Li C, Hu FB, Wirth DF, Song M, Chan AT, Rimm E, Garrett WS, Huttenhower C. A framework for microbiome science in public health. Nat Med. 2021 05; 27(5):766-774. PMID: 33820996.
    Citations: 8     Fields:    Translation:HumansPHPublic Health
  29. McFarland AG, Bertucci HK, Littman E, Shen J, Huttenhower C, Hartmann EM. Triclosan Tolerance Is Driven by a Conserved Mechanism in Diverse Pseudomonas Species. Appl Environ Microbiol. 2021 03 11; 87(7). PMID: 33483311.
    Citations: 2     Fields:    Translation:Cells
  30. Young C, Wood HM, Fuentes Balaguer A, Bottomley D, Gallop N, Wilkinson L, Benton SC, Brealey M, John C, Burtonwood C, Thompson KN, Yan Y, Barrett JH, Morris EJA, Huttenhower C, Quirke P. Microbiome Analysis of More Than 2,000 NHS Bowel Cancer Screening Programme Samples Shows the Potential to Improve Screening Accuracy. Clin Cancer Res. 2021 04 15; 27(8):2246-2254. PMID: 33658300.
    Citations: 1     Fields:    
  31. Borowsky J, Haruki K, Lau MC, Dias Costa A, Väyrynen JP, Ugai T, Arima K, da Silva A, Felt KD, Zhao M, Gurjao C, Twombly TS, Fujiyoshi K, Väyrynen SA, Hamada T, Mima K, Bullman S, Harrison TA, Phipps AI, Peters U, Ng K, Meyerhardt JA, Song M, Giovannucci EL, Wu K, Zhang X, Freeman GJ, Huttenhower C, Garrett WS, Chan AT, Leggett BA, Whitehall VLJ, Walker N, Brown I, Bettington M, Nishihara R, Fuchs CS, Lennerz JK, Giannakis M, Nowak JA, Ogino S. Association of Fusobacterium nucleatum with Specific T-cell Subsets in the Colorectal Carcinoma Microenvironment. Clin Cancer Res. 2021 05 15; 27(10):2816-2826. PMID: 33632927.
    Citations: 8     Fields:    
  32. Young C, Wood HM, Seshadri RA, Van Nang P, Vaccaro C, Melendez LC, Bose M, Van Doi M, Piñero TA, Valladares CT, Arguero J, Balaguer AF, Thompson KN, Yan Y, Huttenhower C, Quirke P. The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries. Genome Med. 2021 02 16; 13(1):27. PMID: 33593386.
    Citations: 3     Fields:    Translation:Humans
  33. Wang DD, Nguyen LH, Li Y, Yan Y, Ma W, Rinott E, Ivey KL, Shai I, Willett WC, Hu FB, Rimm EB, Stampfer MJ, Chan AT, Huttenhower C. The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. Nat Med. 2021 02; 27(2):333-343. PMID: 33574608.
    Citations: 33     Fields:    Translation:HumansCells
  34. Wang Y, Yan Y, Thompson KN, Bae S, Accorsi EK, Zhang Y, Shen J, Vlamakis H, Hartmann EM, Huttenhower C. Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach. Microbiome. 2021 01 21; 9(1):17. PMID: 33478576.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  35. Asnicar F, Berry SE, Valdes AM, Nguyen LH, Piccinno G, Drew DA, Leeming E, Gibson R, Le Roy C, Khatib HA, Francis L, Mazidi M, Mompeo O, Valles-Colomer M, Tett A, Beghini F, Dubois L, Bazzani D, Thomas AM, Mirzayi C, Khleborodova A, Oh S, Hine R, Bonnett C, Capdevila J, Danzanvilliers S, Giordano F, Geistlinger L, Waldron L, Davies R, Hadjigeorgiou G, Wolf J, Ordovás JM, Gardner C, Franks PW, Chan AT, Huttenhower C, Spector TD, Segata N. Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nat Med. 2021 02; 27(2):321-332. PMID: 33432175.
    Citations: 72     Fields:    Translation:HumansAnimalsCellsPHPublic HealthCTClinical Trials
  36. Mitchell CM, Mazzoni C, Hogstrom L, Bryant A, Bergerat A, Cher A, Pochan S, Herman P, Carrigan M, Sharp K, Huttenhower C, Lander ES, Vlamakis H, Xavier RJ, Yassour M. Delivery Mode Affects Stability of Early Infant Gut Microbiota. Cell Rep Med. 2020 12 22; 1(9):100156. PMID: 33377127.
    Citations: 15     Fields:    Translation:HumansCellsPHPublic Health
  37. Accorsi EK, Franzosa EA, Hsu T, Joice Cordy R, Maayan-Metzger A, Jaber H, Reiss-Mandel A, Kline M, DuLong C, Lipsitch M, Regev-Yochay G, Huttenhower C. Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome. Genome Biol. 2020 12 11; 21(1):301. PMID: 33308267.
    Citations: 2     Fields:    Translation:HumansCells
  38. Münch PC, Franzosa EA, Stecher B, McHardy AC, Huttenhower C. Identification of Natural CRISPR Systems and Targets in the Human Microbiome. Cell Host Microbe. 2021 01 13; 29(1):94-106.e4. PMID: 33217332.
    Citations: 3     Fields:    Translation:HumansCells
  39. Nicholson K, Bjornevik K, Abu-Ali G, Chan J, Cortese M, Dedi B, Jeon M, Xavier R, Huttenhower C, Ascherio A, Berry JD. The human gut microbiota in people with amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener. 2021 05; 22(3-4):186-194. PMID: 33135936.
    Citations: 8     Fields:    Translation:HumansCells
  40. Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Med. 2020 08 13; 12(1):71. PMID: 32791981.
    Citations: 17     Fields:    Translation:HumansPHPublic Health
  41. Henn MR, O'Brien EJ, Diao L, Feagan BG, Sandborn WJ, Huttenhower C, Wortman JR, McGovern BH, Wang-Weigand S, Lichter DI, Chafee M, Ford CB, Bernardo P, Zhao P, Simmons S, Tomlinson AD, Cook DN, Pomerantz RJ, Misra BK, Auninš JG, Trucksis M. A Phase 1b Safety Study of SER-287, a Spore-Based Microbiome Therapeutic, for Active Mild to Moderate Ulcerative Colitis. Gastroenterology. 2021 01; 160(1):115-127.e30. PMID: 32763240.
    Citations: 13     Fields:    Translation:HumansCellsCTClinical Trials
  42. Karcher N, Pasolli E, Asnicar F, Huang KD, Tett A, Manara S, Armanini F, Bain D, Duncan SH, Louis P, Zolfo M, Manghi P, Valles-Colomer M, Raffaetà R, Rota-Stabelli O, Collado MC, Zeller G, Falush D, Maixner F, Walker AW, Huttenhower C, Segata N. Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Genome Biol. 2020 06 08; 21(1):138. PMID: 32513234.
    Citations: 18     Fields:    Translation:HumansCells
  43. Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MGI. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol. 2020 06; 38(6):685-688. PMID: 32483366.
    Citations: 329     Fields:    
  44. Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, Zhu Q, Bolzan M, Cumbo F, May U, Sanders JG, Zolfo M, Kopylova E, Pasolli E, Knight R, Mirarab S, Huttenhower C, Segata N. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun. 2020 05 19; 11(1):2500. PMID: 32427907.
    Citations: 47     Fields:    Translation:Cells
  45. Yan Y, Drew DA, Markowitz A, Lloyd-Price J, Abu-Ali G, Nguyen LH, Tran C, Chung DC, Gilpin KK, Meixell D, Parziale M, Schuck M, Patel Z, Richter JM, Kelsey PB, Garrett WS, Chan AT, Stadler ZK, Huttenhower C. Structure of the Mucosal and Stool Microbiome in Lynch Syndrome. Cell Host Microbe. 2020 04 08; 27(4):585-600.e4. PMID: 32240601.
    Citations: 8     Fields:    Translation:HumansCells
  46. Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC. Global chemical effects of the microbiome include new bile-acid conjugations. Nature. 2020 03; 579(7797):123-129. PMID: 32103176.
    Citations: 76     Fields:    Translation:HumansAnimals
  47. Haruki K, Kosumi K, Hamada T, Twombly TS, Väyrynen JP, Kim SA, Masugi Y, Qian ZR, Mima K, Baba Y, da Silva A, Borowsky J, Arima K, Fujiyoshi K, Lau MC, Li P, Guo C, Chen Y, Song M, Nowak JA, Nishihara R, Yanaga K, Zhang X, Wu K, Bullman S, Garrett WS, Huttenhower C, Meyerhardt JA, Giannakis M, Chan AT, Fuchs CS, Ogino S. Association of autophagy status with amount of Fusobacterium nucleatum in colorectal cancer. J Pathol. 2020 04; 250(4):397-408. PMID: 31880318.
    Citations: 10     Fields:    Translation:HumansCells
  48. Ben Maamar S, Glawe AJ, Brown TK, Hellgeth N, Hu J, Wang JP, Huttenhower C, Hartmann EM. Mobilizable antibiotic resistance genes are present in dust microbial communities. PLoS Pathog. 2020 01; 16(1):e1008211. PMID: 31971995.
    Citations: 8     Fields:    Translation:PHPublic Health
  49. Fornelos N, Franzosa EA, Bishai J, Annand JW, Oka A, Lloyd-Price J, Arthur TD, Garner A, Avila-Pacheco J, Haiser HJ, Tolonen AC, Porter JA, Clish CB, Sartor RB, Huttenhower C, Vlamakis H, Xavier RJ. Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease. Nat Microbiol. 2020 03; 5(3):486-497. PMID: 31959971.
    Citations: 14     Fields:    Translation:HumansAnimalsCells
  50. Nguyen LH, Ma W, Wang DD, Cao Y, Mallick H, Gerbaba TK, Lloyd-Price J, Abu-Ali G, Hall AB, Sikavi D, Drew DA, Mehta RS, Arze C, Joshi AD, Yan Y, Branck T, DuLong C, Ivey KL, Ogino S, Rimm EB, Song M, Garrett WS, Izard J, Huttenhower C, Chan AT. Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. Gastroenterology. 2020 04; 158(5):1313-1325. PMID: 31972239.
    Citations: 26     Fields:    Translation:HumansCells
  51. Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nat Commun. 2019 12 02; 10(1):5477. PMID: 31792218.
    Citations: 40     Fields:    Translation:Cells
  52. Tashiro H, Cho Y, Kasahara DI, Brand JD, Bry L, Yeliseyev V, Abu-Ali G, Huttenhower C, Shore SA. Microbiota Contribute to Obesity-related Increases in the Pulmonary Response to Ozone. Am J Respir Cell Mol Biol. 2019 12; 61(6):702-712. PMID: 31144984.
    Citations: 10     Fields:    Translation:AnimalsCells
  53. McBurney MI, Davis C, Fraser CM, Schneeman BO, Huttenhower C, Verbeke K, Walter J, Latulippe ME. Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions. J Nutr. 2019 11 01; 149(11):1882-1895. PMID: 31373365.
    Citations: 48     Fields:    Translation:HumansPHPublic Health
  54. Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, Armanini F, Manghi P, Bonham K, Zolfo M, De Filippis F, Magnabosco C, Bonneau R, Lusingu J, Amuasi J, Reinhard K, Rattei T, Boulund F, Engstrand L, Zink A, Collado MC, Littman DR, Eibach D, Ercolini D, Rota-Stabelli O, Huttenhower C, Maixner F, Segata N. The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. Cell Host Microbe. 2019 11 13; 26(5):666-679.e7. PMID: 31607556.
    Citations: 73     Fields:    Translation:HumansCells
  55. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 Sep; 37(9):1091. PMID: 31399723.
    Citations: 73     Fields:    
  56. Kasahara DI, Wilkinson JE, Cho Y, Cardoso AP, Huttenhower C, Shore SA. The interleukin-33 receptor contributes to pulmonary responses to ozone in male mice: role of the microbiome. Respir Res. 2019 Aug 27; 20(1):197. PMID: 31455422.
    Citations: 9     Fields:    Translation:AnimalsPHPublic Health
  57. Thingholm LB, Rühlemann MC, Koch M, Fuqua B, Laucke G, Boehm R, Bang C, Franzosa EA, Hübenthal M, Rahnavard A, Frost F, Lloyd-Price J, Schirmer M, Lusis AJ, Vulpe CD, Lerch MM, Homuth G, Kacprowski T, Schmidt CO, Nöthlings U, Karlsen TH, Lieb W, Laudes M, Franke A, Huttenhower C. Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition. Cell Host Microbe. 2019 08 14; 26(2):252-264.e10. PMID: 31399369.
    Citations: 63     Fields:    Translation:HumansAnimalsCells
  58. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 08; 37(8):852-857. PMID: 31341288.
    Citations: 2038     Fields:    Translation:Humans
  59. Mallick H, Franzosa EA, Mclver LJ, Banerjee S, Sirota-Madi A, Kostic AD, Clish CB, Vlamakis H, Xavier RJ, Huttenhower C. Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. Nat Commun. 2019 07 17; 10(1):3136. PMID: 31316056.
    Citations: 39     Fields:    Translation:Humans
  60. Dantzler KW, Ma S, Ngotho P, Stone WJR, Tao D, Rijpma S, De Niz M, Nilsson Bark SK, Jore MM, Raaijmakers TK, Early AM, Ubaida-Mohien C, Lemgruber L, Campo JJ, Teng AA, Le TQ, Walker CL, Hermand P, Deterre P, Davies DH, Felgner P, Morlais I, Wirth DF, Neafsey DE, Dinglasan RR, Laufer M, Huttenhower C, Seydel K, Taylor T, Bousema T, Marti M. Naturally acquired immunity against immature Plasmodium falciparum gametocytes. Sci Transl Med. 2019 06 05; 11(495). PMID: 31167926.
    Citations: 16     Fields:    Translation:HumansAnimalsCells
  61. Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron L. HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor. Am J Epidemiol. 2019 06 01; 188(6):1023-1026. PMID: 30649166.