Tamburini S, Clemente JC. "Neonatal gut microbiota induces lung immunity against pneumonia". Nature Reviews Gastroenterology & Hepatology (under review)

Segal LN, Clemente JC, Li Y, Ruan C, Cao J, Danckers-Degregory M, Morris A, Tapyrik S, Diaz P, Calligaro G, Dawson R, van Zyl-Smit RN, Dheda K, Rom WN, Weiden MD. "Anaerobic bacteria fermentation products increase tuberculosis risk in antiretroviral treated HIV-infection". Cell Host & Microbe 2017 (in press)

Walker RW, Clemente JC, Peter I, Faith JJ, Loos, RJ. "The prenatal microbiome. Are we colonized with bacteria in utero?". Pediatric Obesity 2017 (in press)


Scher JU, Vijay J, Artacho A, Abdollahi S, Ockinger J, Kullberg S, Skold M, Eklund A, Grunewald J, Clemente JC, Ubeda C, Segal LN, Catrina AI. “The Lung Microbiota in Early Rheumatoid Arthritis and Autoimmunity”. Microbiome 2016, 4(1):60.

Chudnovskiy A, Mortha A, Kana V, Kennard A, Ramirez JD, Rahman A, Remark R, Mogno I, Ng R, Gnjatic S, Amir ED, Solovyov A, Greenbaum B, Clemente J, Faith J, Belkaid Y, Grigg ME, Merad M. "Host-protozoan interactions protect from mucosal infections through activation of the inflammasome." Cell 2016, 167(2):444-456.

Tamburini S, Clemente JC. "Zooming in on Inflammatory Bowel Disease: Microbial and Proteomic Features Associated With IBD in Colonic Microenvironments." Cellular and Molecular Gastroenterology and Hepatology 2016, 2(5):540-541.

Hoarau G, Mukherjee PK, Gower-Rousseau C, Hager C, Chandra J, Retuerto MA, Neut C, Vermeire S, Clemente JC, Colombel JF, Fujioka H, Poulain D, Sendid B, Ghannoum MA. "Bacteriome and mycobiome interactions underscore microbial dysbiosis in familial Crohn's disease." mBio 2016, 7(5) e01250-16.

Tamburini S, Shen N, Wu HC, Clemente JC. "The microbiome in early life: implications for health outcomes." Nature Medicine 2016, 22(7):713-22.

Segal L, Clemente JC, Wu BG, Wikoff WR, Gao Z, Li Y, Ko J, Rom WN, Blaser MJ, Weiden MD. "Randomized, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung." Thorax 2016, thoraxjnl-2016-208599.

Gacias M, Gaspari S, Mae-Santos P, Tamburini S, Andrade M, Zhang F, Shen N, Tolstikov V, Kiebish MA, Dupree JL, Zachariou V, Clemente JC, Casaccia P. "Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior." Elife 2016, pii: e13442.

Clemente JC, Dominguez-Bello MG. "Safety of vaginal microbial transfer in infants delivered by caesarean, and expected health outcomes." BMJ 2016, 352:i1707.

Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung D, Sampson H, Sicherer S, Clemente JC. "Early-life gut microbiome composition is associated with milk allergy resolution." J Allergy Clin Immunol 2016, S0091-6749(16)30268-8.

Segal LN, Clemente JC, Tsay JJ, Koralov SB, Keller BC, Wu BG, Li Y, Shen N, Ghedin E, Morris A, Diaz P, Huang L, Wikoff WR, Ubeda C, Artacho A, Rom WN, Sterman DH, Collman RG, Blaser MJ, Weiden MD. "Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype." Nature Microbiology 2016, 1:16031.

Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, Bokulich N, Song SJ, Hoashi M, Rivera-Vina J, Mendez K, Knight R, and Clemente JC. “Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer.” Nature Medicine. 2016 Mar;22(3):250-3.


Macklaim JM, Clemente JC, Knight R, Gloor GB, Reid G. “Effect of antimicrobial and probiotic therapy on the vaginal microbiome.” Microbial Ecology in Health and Disease 2015, 26:27799

Haro C, Garcia-Carpintero S, Alcala-Diaz JF, Gomez-Delgado F, Delgado-Lista J, Perez-Martinez P, Rangel Zuñiga OA, Quintana-Navarro GM, Landa BB, Clemente JC, Lopez-Miranda J, Camargo A, Perez-Jimenez F. “The gut microbial community in metabolic syndrome patients is modified by diet.” J Nutr Biochem 2015, S0955-2863(15)00205-3

Shen N and Clemente JC. “Engineering the microbiome: a novel approach to immunotherapy for allergic and immune diseases.” Curr Allergy Asthma Rep 2015, 15(7):538

Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Noya-Alarcon O, Contreras M, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG. “The microbiome of uncontacted Amerindians” Science Advances 2015, 1(3):e1500183

Berg D, Clemente JC, Colombel JF. “Can IBD be Permanently Treated with Short-term Interventions on the Microbiome?” Expert Review of Gastroenterology & Hepatology 2015, 9(6):781-95

Obregon-Tito AJ, Tito RY, Metcalf J, Clemente JC, Ursell LK, Van Treuren W, Knight R, Spicer P, Lawson P, Marin-Reyes L, Trujillo-Villarroel O, Foster M, Guija-Poma E, Troncoso-Corzo L, Amiel J, Ozga A, Lewis CM. “Subsistence strategies in traditional societies distinguish gut microbiomes.” Nature Communications 2015, 6:6505


Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, The Scientists for Advancement of Microbiome Research, White O. “Advancing the Microbiome Research Community.” Cell 2014, 159(2):227–230

Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons S, Chase J, McDonald D, Clemente JC, Gilbert JA, Huse Sm, Zhou H, Knight R, and Caporaso JG. “Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.” PeerJ 2014, 2:e545

Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA, Knight R. “Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity.” Frontiers in Microbiology 2014, 5:298

Bongers G, Lira SA, Clemente JC. “The role of the microbiome in cancer.” Jikken Igaku 2014, 32(5):119-123.

Bongers G, Pacer ME, Geraldino TH, Chen L, He Z, Hashimoto D, Furtado GC, Kelley KA, Clemente JC, Merad M, van Bakel H, and Lira SA. “Interplay of host microbiota, genetic perturbations, and inflammation promote local development of intestinal neoplasms in mice.” Journal of Experimental Medicine 2014, 211(3):457–472.

Manichanh C, Eck A, Varela E, Roca J, Clemente JC, Gonzalez A, Knights D, Knight R, Estrella S, Hernandez C, Guyonnet D, Accarino A, Santos J, Malagelada J, Guarner F, and Azpiroz F. “Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet.” Gut 2013, 63(3):401-8.


Fierer N, Ladau J, Clemente JC, Leff J, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL. “Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States.” Science 2013, 342(6158):621–624.

Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard N, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI. “Gut microbiota from twins discordant for obesity modulate metabolism in mice.” Science 2013, 341(6150):1241213.

Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knighs D, Reyes JA, Clemente JC, Knight R, Beiko RG, Huttenhower C. “Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.” Nature Biotechnology 2013, 31(9):814-21.

Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, Clemente JC, Knight R, Heath AC, Leibel RL, Rosenbaum M, and Gordon JI. “The long-term stability of the human gut microbiota.” Science 2013, 341(6141):1237439.

Segal LN, Alekseyenko A, Clemente JC, Kulkarni R, Wu B, Chung S, Berger K, Goldring R, Rom WN, Aliferis C, Blaser MJ, Weiden MD. “Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation.” Microbiome 2013, 1:19.

Pantoja-Feliciano IG*, Clemente JC*, Costello EK, Perez ME, Blaser MJ, Knight R, and Dominguez-Bello MG. “Biphasic assembly of the murine intestinal microbiota during early development.” ISME 2013, 7:1112–1115 *equal contribution.

Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, Gordon JI and Janssen PH. “Simultaneous amplicon sequencing to explore co-occurrence patterns of prokaryotic and eukaryotic microorganisms in rumen microbial communities.” PLoS ONE 2013, 8(2):e47879.

Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, Knight R. “Cohabiting family members share microbiota with one another, and with their dogs.” eLife 2013 e00458.

Bates ST, Clemente JC, Flores G, Walters WA, Parfrey LW, Knight R, and Fierer N. “Global biogeography of highly diverse protistan communities in soil.” ISME 2013 7(3):652–659.


Stahringer SS, Clemente JC, Corley RP, Hewitt J, Knights D, Walters WA, Knight R and Krauter KS. “Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood.” Genome Research 2012 22(11):2146–2152.

Carvalho FA, Koren O, Johansson M, Nalbantoglu I, Aitken JD, Su Y, Walters WA, Gonzalez A, Clemente JC, Barnich N, Darfeuille-Michaud A, Vijay-Kumar M, Knight R, Ley RE, and Gewirtz AT. “Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice.” Cell Host & Microbe 2012 12(2):139–152.

Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, Gao Z, Clemente JC, Costello EK, Knight R. “Distinct Cutaneous Bacterial Assemblages in a Sampling of South American Amerindians and US Residents.” ISME 2013 7(1):85-95.

McDonald D*, Clemente JC*, Kuczynski J, Rideout JR, Stombaugh J, Walters WA, Wendel D, Wilke A, Huse S, Sogin M, Meyer F, Knight R, and Caporaso JG. “The Biological Observation Matrix (BIOM) Format or: How I Learned To Stop Worrying and Love the Ome-ome.” GigaScience 2012, 1:7. *equal contribution

The Human Microbiome Project Consortium. “Structure, Function and Diversity of the Human Microbiome in an Adult Reference Population.” Nature 2012, 486(7402):207-14.

The Human Microbiome Project Consortium. “A framework for human microbiome research.” Nature 2012, 486(7402):215-21.

Yatsunenko T, Rey F, Manary M, Trehan I, Dominguez-Bello MG, Contreras M, Gris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. “Human gut microbiome differentiation viewed across age and geography.” Nature 2012, 486(7402):222-227.

Clemente JC, Ursell LK, Parfrey LW, Knight R. “The impact of the gut microbiota on human health: an integrative view.” Cell 2012, 148(6):1258–1270.

Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R. “The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites.” Journal of Allergy and Clinical Immunology 2012, 129(5):1204–1208.

Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, Knight R. “Experimental and analytical tools for studying the human microbiome.” Nature Reviews Genetics 2012, 13:47–58.

Tran VA, Jose C. Clemente, Nguyen DT, Li J, Dang XT, Kien Le TT, Anh Nguyen TL, Saethang T, Kubo M, Yamada Y, Satou K. “IMPACT: A novel clustering algorithm based on attraction.” Journal of Computers 2012, 7(3):653–665.


Alonso-Alemany D, Clemente JC, Jansson J, Valiente G. “Taxonomic assignment in metagenomics with TANGO.” EMBnet.journal 2011, 17(2):16–20.

Zaneveld JR, Parfrey LW, Van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh J, Kuckzynski J, Knight R. “Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation.” Trends in Microbiology 2011, 19(10):472-482.

Edgar RC, Haas Bj, Clemente JC, Quince C, Knight R. “UCHIME improves accuracy and speed of chimera detection.” Bioinformatics 2011, 27(16):2194-2200.

Gonzalez A*, Clemente JC*, Shade A*, Metcalf JL, Song SJ, Prithiviraj B, Knight R. “Our microbial selves: what ecology can teach us." EMBO Reports 2011, 12(8):775-784. *equal contribution.

Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A, Fontana L, Henrissat B, Knight R, Gordon JI. “Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans.” Science 2011, 332(6032):970-974.

Birmingham A, Clemente JC, Desai N, Gilbert J, Gonzalez A, Kyrpides N, Meyer F, Nawrocki E, Sterk P, Stombaugh J, Weinberg Z, Wendel D, Leontis NB, Zirbel C, Knight R, Laederach A. “Meeting report of the RNA Ontology Consortium.” Standards in Genomic Science 2011, 4(2).


Clemente JC, Jansson J, Valiente G. “Flexible assignment of ambiguous sequencing reads.” BMC Bioinformatics 2010, 12:8.

Clemente JC, Jansson J, Valiente G. “Accurate taxonomic assignment of short pyrosequencing reads.” In Pacific Symposium on Biocomputing (PSB) 2010, 3–9.


Clemente JC, Ikeo K, Valiente G, Gojobori T. “Optimized ancestral reconstruction using Sankoff parsimony.” BMC Bioinformatics 2009, 10:51.

Gojobori T, Nakagawa S, Clemente JC. “DNA sequence analysis.” In Encyclopedia of Life Sciences 2009, John Wiley & Sons, Ltd: Chichester.

Gojobori T, Kinjo S, Clemente JC, Ikeo K. “Strategic construction of databases in the era of the so-called next generation sequencers.” Jikken Igaku 2009, 27(1):32–37