Faculty Profile

Dr. Libusha Kelly, Ph.D.

Libusha Kelly, Ph.D.

Assistant Professor, Department of Systems & Computational Biology

Assistant Professor, Department of Microbiology & Immunology

Areas of Research: Xenobiotic metabolism by the gut microbiome in adverse drug responses; Pharmacokinetics of the gut microbiome; Influence of phage and other mobile genetic elements on microbial ecosystem metabolic and functional capacity.

Professional Interests

Our lab is at the forefront of microbial ecology, studying the interplay between diversity and functional capacity in natural microbial communities.

We focus on: 1) the capacity for microbes to metabolize excreted drugs in human populations, and 2) the influence of mobile element pools on microbial ecosystem functional capacity.

Microbial genomes harbor tremendous diversity at the gene level even within closely related taxonomic groups. Microbes exchange DNA, with each other and with viruses, and can also take up DNA from the environment, leading to variability in the functional capacity of individual cells. Microbial ecosystems, therefore, are a social network of interacting and mobile genes with the capacity for tremendous functional plasticity. Microbes in the gut carry enzymes with the potential to metabolize excreted drugs, some of which cause adverse drug responses in patients. We study the abundance and phylogenetic distribution of microbial enzymes in human guts to predict the capacity of patients to metabolize drugs.  Our focus is on the question:  what forces enable genetic mobility, or information flow, in microbial ecosystems and how do these forces contribute to the evolution of community functions?

We work with microbial communities from marine systems and the human gut. The specific goals of the lab are to develop a pharmacokinetics of the human microbiome by incorporating the many enzymes with the potential to interact with excreted drugs; and to predict gene mobility and spread to enable targeted manipulation of the metabolic capacity of microbial communities in diverse environments

Visit our lab website: http://www.kellylab.org/

Selected Publications


For a complete list see:


† indicates authors contributed equally to the work

Kelly L, Ding H, Huang KH, Osburne MS, Chisholm SW. Genetic diversity in cultured and wild marinecyanomyoviruses reveals phosphorus stress as a strong selective agent. ISME J. 2013 May 9. doi:10.1038/ismej.2013.58.

Kelly L†, Huang KH†, Ding H, Chisholm SW. ProPortal: A resource for integrated systems biology of Prochlorococcus and its phage. Nucleic Acids Res. 2012 Jan;40(Database issue):D632-40.

Malmstrom RR†, Rodrigue S†, Huang KH, Kelly L, Kern SE, Thompson A, Roggensack S, Berube PM, Henn MR, Chisholm SW. Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. ISME J. 2012 Aug 16.

Thompson LR†, Zeng Q†, Kelly L, Huang KH, Singer AU, Stubbe J, Chisholm SW. Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):E757-64.

B. Li†, D. Sher†, L. Kelly, Y. Shi, K. Huang, P. J. Knerr, I. Joewono, D. Rusch, S. W. Chisholm, and W. A. van der Donk, “Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria.,” Proc Natl Acad Sci U S A, vol. 107, no. 23, pp. 10430–10435, Jun. 2010.

L. Kelly, R. Karchin, and A. Sali, “Protein interactions and disease phenotypes in the ABC transporter superfamily.,” Pac Symp Biocomput, 2007.

L. Kelly, U. Pieper, N. Eswar, F. A. Hays, M. Li, Z. Roe-Zurz, D. L. Kroetz, K. M. Giacomini, R. M. Stroud, and A. Sali, “A survey of integral alpha-helical membrane proteins,” J Struct Funct Genomics, vol. 10, no. 4, pp. 269–280, Dec. 2009. PMCID: PMC2780624

L. Kelly†, H. Fukushima†, R. Karchin, J. M. Gow, L. W. Chinn, U. Pieper, M. R. Segal, D. L. Kroetz, and A. Sali, “Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains.,” Protein Sci, vol. 19, no. 11, pp. 2110–2121, Nov. 2010.


More Information About Dr. Libusha Kelly

Kelly Lab Website

Material in this section is provided by individual faculty members who are solely responsible for its accuracy and content.

Albert Einstein College of Medicine
Michael F. Price Center
1301 Morris Park Avenue , Room 553B
Bronx, NY 10461

Tel: 718.678.1148
Fax: 718.678.1022

Research Information

In the News

The Atlantic quotes Dr. Libusha Kelly on how some bacteria may protect tumors from anticancer drugs.

Nature interviews Dr. Libusha Kelly and graduate student Leah Guthrie about their study on individuals’ microbiomes and their effect on the body’s metabolism of the chemotherapy drug irinotecan.

More media coverage