Rob Knight

Professor
Ph.D., Princeton University
Email: robknight@ucsd.edu

Research Interests:

Human microbiome; microbial community ecology; multi-omics analyses.

Track(s)

Microbiology/Immunology

Genetics

BMS Focus Areas:

Bioinformatics

Glycobiology

Selected Publications:

See full list at: Google Scholar

Examples include:

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.

Bacteria from diverse habitats colonize and compete in the mouse gut.

Seedorf H, Griffin NW, Ridaura VK, Reyes A, Cheng J, Rey FE, Smith MI, Simon GM, Scheffrahn RH, Woebken D, Spormann AM, Van Treuren W, Ursell LK, Pirrung M, Robbins-Pianka A, Cantarel BL, Lombard V, Henrissat B, Knight R, Gordon JI.

Cell. 2014 Oct 9;159(2):253-66. doi: 10.1016/j.cell.2014.09.008. Epub 2014 Oct 2.

Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA.

Science. 2014 Aug 29;345(6200):1048-52. doi: 10.1126/science.1254529.

SnapShot: the human microbiome.

González A, Vázquez-Baeza Y, Knight R.

Cell. 2014 Jul 31;158(3):690-690.e1. doi: 10.1016/j.cell.2014.07.019. No abstract available. 

Conducting a microbiome study.

Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE.

Cell. 2014 Jul 17;158(2):250-62. doi: 10.1016/j.cell.2014.06.037.

Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota.

Kashyap PC, Marcobal A, Ursell LK, Smits SA, Sonnenburg ED, Costello EK, Higginbottom SK, Domino SE, Holmes SP, Relman DA, Knight R, Gordon JI, Sonnenburg JL.

Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):17059-64. doi: 10.1073/pnas.1306070110. Epub 2013 Sep 23.

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.

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.

Gut microbiomes of Malawian twin pairs discordant for kwashiorkor.

Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC, Liu J, Houpt E, Li JV, Holmes E, Nicholson J, Knights D, Ursell LK, Knight R, Gordon JI.

Science. 2013 Feb 1;339(6119):548-54. doi: 10.1126/science.1229000. Epub 2013 Jan 30.

Diversity, stability and resilience of the human gut microbiota.

Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R.

Nature. 2012 Sep 13;489(7415):220-30. doi: 10.1038/nature11550. Review.

Host remodeling of the gut microbiome and metabolic changes during pregnancy.

Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Bäckhed HK, Gonzalez A, Werner JJ, Angenent LT, Knight R, Bäckhed F, Isolauri E, Salminen S, Ley RE.

Cell. 2012 Aug 3;150(3):470-80. doi: 10.1016/j.cell.2012.07.008.

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.

A framework for human microbiome research.

Human Microbiome Project Consortium.

Nature. 2012 Jun 13;486(7402):215-21. doi: 10.1038/nature11209.

Structure, function and diversity of the healthy human microbiome.

Human Microbiome Project Consortium.

Nature. 2012 Jun 13;486(7402):207-14. doi: 10.1038/nature11234.

The impact of the gut microbiota on human health: an integrative view.

Clemente JC, Ursell LK, Parfrey LW, Knight R.

Cell. 2012 Mar 16;148(6):1258-70. doi: 10.1016/j.cell.2012.01.035. Review.

Linking long-term dietary patterns with gut microbial enterotypes.

Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD.

Science. 2011 Oct 7;334(6052):105-8. doi: 10.1126/science.1208344. Epub 2011 Sep 1.

Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans.

Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI.

Science. 2011 May 20;332(6032):970-4. doi: 10.1126/science.1198719.

Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins.

Hansen EE, Lozupone CA, Rey FE, Wu M, Guruge JL, Narra A, Goodfellow J, Zaneveld JR, McDonald DT, Goodrich JA, Heath AC, Knight R, Gordon JI.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4599-606. doi: 10.1073/pnas.1000071108. Epub 2011 Feb 11.

Human oral, gut, and plaque microbiota in patients with atherosclerosis.

Koren O, Spor A, Felin J, Fåk F, Stombaugh J, Tremaroli V, Behre CJ, Knight R, Fagerberg B, Ley RE, Bäckhed F.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4592-8. doi: 10.1073/pnas.1011383107. Epub 2010 Oct 11.

Succession of microbial consortia in the developing infant gut microbiome.

Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT, Ley RE.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4578-85. doi: 10.1073/pnas.1000081107. Epub 2010 Jul 28.

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns.

Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R.

Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):11971-5. doi: 10.1073/pnas.1002601107. Epub 2010 Jun 21.

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins.

Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, Affourtit J, Egholm M, Henrissat B, Knight R, Gordon JI.

Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7503-8. doi: 10.1073/pnas.1002355107. Epub 2010 Apr 2.

Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5.

Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, Sitaraman SV, Knight R, Ley RE, Gewirtz AT.

Science. 2010 Apr 9;328(5975):228-31. doi: 10.1126/science.1179721. Epub 2010 Mar 4.

Bacterial community variation in human body habitats across space and time.

Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R.

Science. 2009 Dec 18;326(5960):1694-7. doi: 10.1126/science.1177486. Epub 2009 Nov 5.

Crawford PA, Crowley JR, Sambandam N, Muegge BD, Costello EK, Hamady M, Knight R, Gordon JI.

Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11276-81. doi: 10.1073/pnas.0902366106. Epub 2009 Jun 22.

A core gut microbiome in obese and lean twins.

Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI.

Nature. 2009 Jan 22;457(7228):480-4. doi: 10.1038/nature07540. Epub 2008 Nov 30.

The influence of sex, handedness, and washing on the diversity of hand surface bacteria.

Fierer N, Hamady M, Lauber CL, Knight R.

Proc Natl Acad Sci U S A. 2008 Nov 18;105(46):17994-9. doi: 10.1073/pnas.0807920105. Epub 2008 Nov 12.

The convergence of carbohydrate active gene repertoires in human gut microbes.

Lozupone CA, Hamady M, Cantarel BL, Coutinho PM, Henrissat B, Gordon JI, Knight R.

Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):15076-81. doi: 10.1073/pnas.0807339105. Epub 2008 Sep 19.

Evolution of mammals and their gut microbes.

Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI.

Science. 2008 Jun 20;320(5883):1647-51. doi: 10.1126/science.1155725. Epub 2008 May 22.

The human microbiome project.

Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI.

Nature. 2007 Oct 18;449(7164):804-10.

Obesity alters gut microbial ecology.

Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI.

Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):11070-5. Epub 2005 Jul 20.