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Translating microbiome futures.

Taroncher-Oldenburg G, Jones S, Blaser M, Bonneau R, Christey P, Clemente JC, Elinav E, Ghedin E, Huttenhower C, Kelly D, Kyle D, Littman D, Maiti A, Maue A, Olle B, Segal L, van Hylckama Vlieg JET, Wang J.

Nat Biotechnol. 2018 Nov 9;36(11):1037-1042. doi: 10.1038/nbt.4287. No abstract available.


Evaluation of the airway microbiome in nontuberculous mycobacteria disease.

Sulaiman I, Wu BG, Li Y, Scott AS, Malecha P, Scaglione B, Wang J, Basavaraj A, Chung S, Bantis K, Carpenito J, Clemente JC, Shen N, Bessich J, Rafeq S, Michaud G, Donington J, Naidoo C, Theron G, Schattner G, Garofano S, Condos R, Kamelhar D, Addrizzo-Harris D, Segal LN.

Eur Respir J. 2018 Oct 25;52(4). pii: 1800810. doi: 10.1183/13993003.00810-2018. Print 2018 Oct.


Physical Activity, Immune System, and the Microbiome in Cardiovascular Disease.

Fernandez DM, Clemente JC, Giannarelli C.

Front Physiol. 2018 Jun 29;9:763. doi: 10.3389/fphys.2018.00763. eCollection 2018.


Severe Obstructive Sleep Apnea is Associated with Alterations in the Nasal Microbiome and Increase in Inflammation.

Wu BG, Sulaiman I, Wang J, Shen N, Clemente JC, Li Y, Laumbach RJ, Lu SE, Udasin I, Le-Hoang O, Perez A, Alimokhtari S, Black K, Plietz M, Twumasi A, Sanders H, Malecha P, Kapoor B, Scaglione BD, Wang A, Blazoski C, Weiden MD, Rapoport DM, Harrison D, Chitkara N, Vicente E, Marin JM, Sunderram J, Ayappa I, Segal LN.

Am J Respir Crit Care Med. 2018 Jul 3. doi: 10.1164/rccm.201801-0119OC. [Epub ahead of print]


Diet Modifies Colonic Microbiota and CD4+ T-Cell Repertoire to Induce Flares of Colitis in Mice With Myeloid-Cell Expression of Interleukin 23.

Chen L, He Z, Iuga AC, Martins Filho SN, Faith JJ, Clemente JC, Deshpande M, Jayaprakash A, Colombel JF, Lafaille JJ, Sachidanandam R, Furtado GC, Lira SA.

Gastroenterology. 2018 Oct;155(4):1177-1191.e16. doi: 10.1053/j.gastro.2018.06.034. Epub 2018 Jun 15.


Airway Microbiota Is Associated with Upregulation of the PI3K Pathway in Lung Cancer.

Tsay JJ, Wu BG, Badri MH, Clemente JC, Shen N, Meyn P, Li Y, Yie TA, Lhakhang T, Olsen E, Murthy V, Michaud G, Sulaiman I, Tsirigos A, Heguy A, Pass H, Weiden MD, Rom WN, Sterman DH, Bonneau R, Blaser MJ, Segal LN.

Am J Respir Crit Care Med. 2018 Nov 1;198(9):1188-1198. doi: 10.1164/rccm.201710-2118OC.


The role of the gut microbiome in systemic inflammatory disease.

Clemente JC, Manasson J, Scher JU.

BMJ. 2018 Jan 8;360:j5145. doi: 10.1136/bmj.j5145. Review.


Interactions Between Diet and the Intestinal Microbiota Alter Intestinal Permeability and Colitis Severity in Mice.

Llewellyn SR, Britton GJ, Contijoch EJ, Vennaro OH, Mortha A, Colombel JF, Grinspan A, Clemente JC, Merad M, Faith JJ.

Gastroenterology. 2018 Mar;154(4):1037-1046.e2. doi: 10.1053/j.gastro.2017.11.030. Epub 2017 Nov 23.


Gut Microbiota Perturbations in Reactive Arthritis and Postinfectious Spondyloarthritis.

Manasson J, Shen N, Garcia Ferrer HR, Ubeda C, Iraheta I, Heguy A, Von Feldt JM, Espinoza LR, Garcia Kutzbach A, Segal LN, Ogdie A, Clemente JC, Scher JU.

Arthritis Rheumatol. 2018 Feb;70(2):242-254. doi: 10.1002/art.40359. Epub 2018 Jan 3.


Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus.

Dahl C, Stanislawski M, Iszatt N, Mandal S, Lozupone C, Clemente JC, Knight R, Stigum H, Eggesbø M.

PLoS One. 2017 Oct 25;12(10):e0184336. doi: 10.1371/journal.pone.0184336. eCollection 2017.


Consumption of Two Healthy Dietary Patterns Restored Microbiota Dysbiosis in Obese Patients with Metabolic Dysfunction.

Haro C, García-Carpintero S, Rangel-Zúñiga OA, Alcalá-Díaz JF, Landa BB, Clemente JC, Pérez-Martínez P, López-Miranda J, Pérez-Jiménez F, Camargo A.

Mol Nutr Food Res. 2017 Dec;61(12). doi: 10.1002/mnfr.201700300. Epub 2017 Nov 7.


The excessive caloric intake and micronutrient deficiencies related to obesity after a long-term interdisciplinary therapy.

Poli VFS, Sanches RB, Moraes ADS, Fidalgo JPN, Nascimento MA, Bresciani P, Andrade-Silva SG, Cipullo MAT, Clemente JC, Caranti DA.

Nutrition. 2017 Jun;38:113-119. doi: 10.1016/j.nut.2017.01.012. Epub 2017 Feb 24.


The prenatal gut microbiome: are we colonized with bacteria in utero?

Walker RW, Clemente JC, Peter I, Loos RJF.

Pediatr Obes. 2017 Aug;12 Suppl 1:3-17. doi: 10.1111/ijpo.12217. Epub 2017 Apr 26. Review.


Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV Patients.

Segal LN, Clemente JC, Li Y, Ruan C, Cao J, Danckers M, Morris A, Tapyrik S, Wu BG, Diaz P, Calligaro G, Dawson R, van Zyl-Smit RN, Dheda K, Rom WN, Weiden MD.

Cell Host Microbe. 2017 Apr 12;21(4):530-537.e4. doi: 10.1016/j.chom.2017.03.003. Epub 2017 Mar 30.


Gut microbiota: Neonatal gut microbiota induces lung immunity against pneumonia.

Tamburini S, Clemente JC.

Nat Rev Gastroenterol Hepatol. 2017 May;14(5):263-264. doi: 10.1038/nrgastro.2017.34. Epub 2017 Mar 22. No abstract available.


Zooming in on Inflammatory Bowel Disease: Microbial and Proteomic Features Associated With IBD in Colonic Microenvironments.

Tamburini S, Clemente JC.

Cell Mol Gastroenterol Hepatol. 2016 Jul 26;2(5):540-541. doi: 10.1016/j.jcmgh.2016.07.001. eCollection 2016 Sep. No abstract available.


The lung microbiota in early rheumatoid arthritis and autoimmunity.

Scher JU, Joshua V, Artacho A, Abdollahi-Roodsaz S, Öckinger J, Kullberg S, Sköld M, Eklund A, Grunewald J, Clemente JC, Ubeda C, Segal LN, Catrina AI.

Microbiome. 2016 Nov 17;4(1):60.


Resting energy expenditure in obese women: comparison between measured and estimated values.

Poli VF, Sanches RB, Moraes AD, Fidalgo JP, Nascimento MA, Andrade-Silva SG, Clemente JC, Yi LC, Caranti DA.

Br J Nutr. 2016 Oct;116(7):1306-1313. Epub 2016 Sep 19.


Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype.

Segal LN, Clemente JC, Tsay JC, 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.

Nat Microbiol. 2016 Apr 4;1:16031. doi: 10.1038/nmicrobiol.2016.31.


Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung.

Segal LN, Clemente JC, Wu BG, Wikoff WR, Gao Z, Li Y, Ko JP, Rom WN, Blaser MJ, Weiden MD.

Thorax. 2017 Jan;72(1):13-22. doi: 10.1136/thoraxjnl-2016-208599. Epub 2016 Aug 2.


The microbiome in early life: implications for health outcomes.

Tamburini S, Shen N, Wu HC, Clemente JC.

Nat Med. 2016 Jul 7;22(7):713-22. doi: 10.1038/nm.4142. Review.


Early-life gut microbiome composition and milk allergy resolution.

Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S, Clemente JC.

J Allergy Clin Immunol. 2016 Oct;138(4):1122-1130. doi: 10.1016/j.jaci.2016.03.041. Epub 2016 May 10.


Intestinal Microbiota Is Influenced by Gender and Body Mass Index.

Haro C, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, Delgado-Lista J, Quintana-Navarro GM, Landa BB, Navas-Cortés JA, Tena-Sempere M, Clemente JC, López-Miranda J, Pérez-Jiménez F, Camargo A.

PLoS One. 2016 May 26;11(5):e0154090. doi: 10.1371/journal.pone.0154090. eCollection 2016.


Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior.

Gacias M, Gaspari S, Santos PM, Tamburini S, Andrade M, Zhang F, Shen N, Tolstikov V, Kiebish MA, Dupree JL, Zachariou V, Clemente JC, Casaccia P.

Elife. 2016 Apr 20;5. pii: e13442. doi: 10.7554/eLife.13442.


Safety of vaginal microbial transfer in infants delivered by caesarean, and expected health outcomes.

Clemente JC, Dominguez-Bello MG.

BMJ. 2016 Mar 31;352:i1707. doi: 10.1136/bmj.i1707. No abstract available.


Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer.

Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, Bokulich NA, Song SJ, Hoashi M, Rivera-Vinas JI, Mendez K, Knight R, Clemente JC.

Nat Med. 2016 Mar;22(3):250-3. doi: 10.1038/nm.4039. Epub 2016 Feb 1.


The gut microbial community in metabolic syndrome patients is modified by diet.

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.

J Nutr Biochem. 2016 Jan;27:27-31. doi: 10.1016/j.jnutbio.2015.08.011. Epub 2015 Aug 20.


Changes in vaginal microbiota following antimicrobial and probiotic therapy.

Macklaim JM, Clemente JC, Knight R, Gloor GB, Reid G.

Microb Ecol Health Dis. 2015 Aug 14;26:27799. doi: 10.3402/mehd.v26.27799. eCollection 2015.


The microbiome of uncontacted Amerindians.

Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcón Ó, Lander O, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Shen N, Song SJ, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG.

Sci Adv. 2015 Apr 3;1(3). pii: e1500183.


Engineering the Microbiome: a Novel Approach to Immunotherapy for Allergic and Immune Diseases.

Shen N, Clemente JC.

Curr Allergy Asthma Rep. 2015 Jul;15(7):39. doi: 10.1007/s11882-015-0538-9. Review.


Subsistence strategies in traditional societies distinguish gut microbiomes.

Obregon-Tito AJ, Tito RY, Metcalf J, Sankaranarayanan K, Clemente JC, Ursell LK, Zech Xu Z, Van Treuren W, Knight R, Gaffney PM, Spicer P, Lawson P, Marin-Reyes L, Trujillo-Villarroel O, Foster M, Guija-Poma E, Troncoso-Corzo L, Warinner C, Ozga AT, Lewis CM.

Nat Commun. 2015 Mar 25;6:6505. doi: 10.1038/ncomms7505.


Can inflammatory bowel disease be permanently treated with short-term interventions on the microbiome?

Berg D, Clemente JC, Colombel JF.

Expert Rev Gastroenterol Hepatol. 2015 Jun;9(6):781-95. doi: 10.1586/17474124.2015.1013031. Epub 2015 Feb 10. Review.


Advancing the microbiome research community.

Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J; Scientists for Advancement of Microbiome Research, White O.

Cell. 2014 Oct 9;159(2):227-30. doi: 10.1016/j.cell.2014.09.022.


Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.

Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou HW, Knight R, Caporaso JG.

PeerJ. 2014 Aug 21;2:e545. doi: 10.7717/peerj.545. eCollection 2014.


Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity.

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.

Front Microbiol. 2014 Jun 19;5:298. doi: 10.3389/fmicb.2014.00298. eCollection 2014.


Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice.

Bongers G, Pacer ME, Geraldino TH, Chen L, He Z, Hashimoto D, Furtado GC, Ochando J, Kelley KA, Clemente JC, Merad M, van Bakel H, Lira SA.

J Exp Med. 2014 Mar 10;211(3):457-72. doi: 10.1084/jem.20131587. Epub 2014 Mar 3.


Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation.

Segal LN, Alekseyenko AV, Clemente JC, Kulkarni R, Wu B, Gao Z, Chen H, Berger KI, Goldring RM, Rom WN, Blaser MJ, Weiden MD.

Microbiome. 2013 Jul 1;1(1):19. doi: 10.1186/2049-2618-1-19. Erratum in: Microbiome. 2014;2:21. Gao, Zhan [added].


Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States.

Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL.

Science. 2013 Nov 1;342(6158):621-4. doi: 10.1126/science.1243768.


Gut microbiota from twins discordant for obesity modulate metabolism in mice.

Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, 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.

Science. 2013 Sep 6;341(6150):1241214. doi: 10.1126/science.1241214.


Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C.

Nat Biotechnol. 2013 Sep;31(9):814-21. doi: 10.1038/nbt.2676. Epub 2013 Aug 25.


The long-term stability of the human gut microbiota.

Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, Clemente JC, Knight R, Heath AC, Leibel RL, Rosenbaum M, Gordon JI.

Science. 2013 Jul 5;341(6141):1237439. doi: 10.1126/science.1237439.


Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet.

Manichanh C, Eck A, Varela E, Roca J, Clemente JC, González A, Knights D, Knight R, Estrella S, Hernandez C, Guyonnet D, Accarino A, Santos J, Malagelada JR, Guarner F, Azpiroz F.

Gut. 2014 Mar;63(3):401-8. doi: 10.1136/gutjnl-2012-303013. Epub 2013 Jun 13.


Cohabiting family members share microbiota with one another and with their dogs.

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.

Elife. 2013 Apr 16;2:e00458. doi: 10.7554/eLife.00458.


Biphasic assembly of the murine intestinal microbiota during early development.

Pantoja-Feliciano IG, Clemente JC, Costello EK, Perez ME, Blaser MJ, Knight R, Dominguez-Bello MG.

ISME J. 2013 Jun;7(6):1112-5. doi: 10.1038/ismej.2013.15. Epub 2013 Mar 28.


Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities.

Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, Gordon JI, Janssen PH.

PLoS One. 2013;8(2):e47879. doi: 10.1371/journal.pone.0047879. Epub 2013 Feb 8.


Global biogeography of highly diverse protistan communities in soil.

Bates ST, Clemente JC, Flores GE, Walters WA, Parfrey LW, Knight R, Fierer N.

ISME J. 2013 Mar;7(3):652-9. doi: 10.1038/ismej.2012.147. Epub 2012 Dec 13.


Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood.

Stahringer SS, Clemente JC, Corley RP, Hewitt J, Knights D, Walters WA, Knight R, Krauter KS.

Genome Res. 2012 Nov;22(11):2146-52. doi: 10.1101/gr.140608.112. Epub 2012 Oct 12.


Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents.

Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, Gao Z, Clemente JC, Costello EK, Knight R.

ISME J. 2013 Jan;7(1):85-95. doi: 10.1038/ismej.2012.81. Epub 2012 Aug 16.


Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice.

Carvalho FA, Koren O, Goodrich JK, Johansson ME, Nalbantoglu I, Aitken JD, Su Y, Chassaing B, Walters WA, González A, Clemente JC, Cullender TC, Barnich N, Darfeuille-Michaud A, Vijay-Kumar M, Knight R, Ley RE, Gewirtz AT.

Cell Host Microbe. 2012 Aug 16;12(2):139-52. doi: 10.1016/j.chom.2012.07.004. Epub 2012 Aug 2.


Human gut microbiome viewed across age and geography.

Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris 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.

Nature. 2012 May 9;486(7402):222-7. doi: 10.1038/nature11053.

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