Faculty Profile

Dr. Libusha Kelly, Ph.D.

Libusha Kelly, Ph.D.

Associate Professor, Department of Systems & Computational Biology

Associate Professor, Department of Microbiology & Immunology

Areas of Research: food and drug metabolism by the gut microbiome; microbial pharmacokinetics; adverse drug responses and the microbiome; phage/host interactions; phage discovery; marine microbiology; microbial ecology

Professional Interests

The Kelly lab: understanding microbial population dynamics to improve human health.

Our basic research program develops new experimental and computational technologies to biologically organize and describe the dynamics of the tremendous genetic diversity in microbial communities. Microbes and viruses are first responders to alterations in the environment. Microbial responses to environmental changes include transcriptional, proliferative, and genomic changes little is known about how viruses respond to environmental perturbations in the context of interactions with their hosts. Furthermore, microbes and viruses exist in tight-knit networks that compete for, produce, and share resources. Microbial community structure/function relationships are poorly understood, which inhibits our ability to support or prevent particular functions. We develop new computational methods to 1) quantify genomic differences and interactions in microbial and viral populations and 2) characterize novel viruses. We recently reported in Nature a novel family of tailless viruses that are major unrecognized killers of marine viruses with the Polz lab at MIT (Kauffman, et al. 2017). These mysterious viruses are also found in the human microbiome, and we are in the process of characterizing their effects on microbial communities in the human body. If we understand how communities are organized and how they change over time under particular conditions, such as inflammation, we can better target microbes and genes to alter that condition.

Our translational research program provides patients and their doctors with actionable information about their microbiomes to improve health and treatment plans. For example, we recently discovered that microbiomes of different individuals have different capacities to activate irinotecan, an anti-cancer drug (Guthrie, et al, 2017). We linked this differential metabolism to specific microbial carbohydrate active enzymes. In mouse models, gut metabolism of irinotecan leads to adverse events, including severe diarrhea. We hypothesize that the life- threatening diarrhea that afflicts up to a quarter of metastatic colorectal cancer patients who take this drug might also be caused by microbial turnover, and are working with oncologists at Einstein/Montefiore to recruit and track patients receiving regimens that include irinotecan. Our goal is to provide patients with early warnings that they are likely high irinotecan metabolizers, thereby enabling prophylactic diarrheal treatment and closer monitoring by their treatment team. A tantalizing possibility here is to use a dietary carbon source to saturate the drug- interacting carbohydrate active enzymes before patients are given the drug, thereby reducing the number of patients who suspend treatment due to severe adverse events.

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

Selected Publications

For a complete list see:


† indicates authors contributed equally to the work

Kauffman KM, Hussain FA, Yang J, Arevalo P, Brown JM, Chang WK, VanInsberghe D, Elsherbini J, Sharma RS, Cutler MB, Kelly L*, Polz MF*. A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria. Nature. 2018 Feb 1 554(7690):118-122. doi: 10.1038/nature25474.  (*=co-corresponding author)

Guthrie L, Gupta S, Daily J, Kelly L. Human microbiome signatures of differential colorectal cancer drug metabolism. NPJ Biofilms Microbiomes. 2017 Nov 1 3:27. doi: 10.1038/s41522-017-0034-1. eCollection 2017. PubMed PMID:29104759 PubMed Central PMCID: PMC5665930.

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.

Li B†, Sher D†, Kelly L, Shi Y, Huang K, Knerr PJ, Joewono I, Rusch D, Chisholm SW, van der Donk WA. Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria. Proc Natl Acad Sci U S A. 2010 Jun 8 107(23):10430-5. doi: 10.1073/pnas.0913677107.

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. doi:10.1073/pnas.1102164108. 

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. 

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

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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

Gut Bacteria Feast on the Pills We Pop

Libusha Kelly, Ph.D., whose lab investigates how the gut microbiome interacts with different drugs, explains how microbes act “like tiny chemists.” Dr. Kelly is associate professor of systems & computational biology and of microbiology & immunology.

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

More media coverage