Professor, Pediatrics and Computer Science & Engineering
University of California, San Diego


Rob Knight is integrating concepts from evolutionary biology and ecology with high-throughput sequencing to study molecular diversity. He is especially interested in understanding how the human microbiome develops and how variation in the microbiome affects health and disease.


Rob Knight got his PhD 10 years ago in ecology and evolutionary biology and quickly became involved in the study of bacterial communities on and in the human body. In addition to pursuing his basic research, he is working with Jeffrey I. Gordon at Washington University to set up a translational medicine pipeline in Malawi and Bangladesh—with the help of the Gates Foundation—to study microbiomes related to such diseases of malnutrition as kwashiorkor and marasmus.The goal is to treat these illnesses by restoring altered microbial communities.

Our goal is to understand biological evolution at scales ranging from individual molecules to whole ecosystems. We use a combination of techniques drawn from fields ranging from computer science to molecular biology to understand the evolution, structure, and function of the human microbiome (the microbes that inhabit each of our bodies) and, at a more fundamental level, the evolution of biochemical functions in random-sequence pools of RNA molecules.


Hecht, G.A., Blaser, M.J., Gordon, J., Kaplan, L.M., Knight, R., Laine, L., Peek, R., Sanders, M.E., Sartor, B., Wu, G.D., Yang, V.W. (2013) “What's the Value of an FDA IND for Fecal Microbiota Transplantation in Clostridium difficile Infection?” Clin Gastroenterol Hepatol. 2013 Oct 19.

Schriml, L., Mizrachi, I., Sterl, P., Field, D., Hirschman, L., Tatusova, T., Sansone, S., Gilbert, J., Schindel, D., Davies, N., Meyer, C., Meyer, F., Garrity, G., Proctor, L., Medema, M., Lan, Y., Klindworth, A., Glöckner, F.O., Korves, T., Gonzalez, A., Dwayndt, P., Göker, M., Johnston, A., Pafilis, E., Schneider, S., Baker, K., Parr, C., Sutton, G., Creasy, H., Kyrpides, N., Wommack, K.E., Whetzel, P.L., Nasko, D., Lapp, H., Fujisawa, T., Phillippy, A.M., Kottman, R., Blake, J.A., Li, J., Glass, E.M., ten Hoopen, P., Knight, R., Holmes, S., Huttenhower, C., Salzberg, S.L., Ma, B., White, O. (2013) “The 15th Genomic Standards Consortium meeting” Standards in Genomic Sciences 8 (1).

Bates, S.T., Ahrendt, S., Bik, H.M., Bruns, T.D., Caporaso, J.G., Cole, J., Dwan, M., Fierer, N., Gu, D., Houston, S., Knight, R., Leff, J., Lewis, C., Maestre, J.P., McDonald, D., Nilsson, R.H., Porras-Alfaro, A., Robert, V., Schoch, C., Scott, J., Taylor, D.L., Parfrey, L.W., Stajich, J.E. (2013) “Meeting report: fungal its workshop (october 2012).“ Stand Genomic Sci. 2013 Apr 15;8(1):118-23.

Smith, D., Alverdy, J., An, G., Coleman, M., Garcia-Houchins, S., Green, J., Keegan, K., Kelley, S.T., Kirkup, B.C., Kociolek, L., Levin, H., Landon, E., Olsiewski, P., Knight, R., Siegel, J., Weber, S., Gilbert, J. (2013) “The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012.“ Stand Genomic Sci. 2013 Apr 15;8(1):112-7.

Brown, J., de Vos, W.M., Distefano, P.S., Doré, J., Huttenhower, C., Knight, R., Lawley, T.D., Raes, J., Turnbaugh, P. (2013) “Translating the human microbiome.” Nat Biotechnol. 2013 Apr;31(4):304-8.



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