Joseph P. Zackular, PhD

Assistant Professor of Pathology and Laboratory Medicine
Assistant Professor of Microbiology
Perelman School of Medicine at the University of Pennsylvania

Contact Information1211A Abramson Research Center
3615 Civic Center Blvd
Philadelphia, PA, 19104
Office: 267-426-5016


Specialty Division

Immunobiology and Experimental Pathology

Research Expertise

The overall goal of the Zackular laboratory is to understand how interactions between the host, gut microbiota, and pathogenic microbes impact human health and disease. At the center of our research is the important nosocomial pathogen, Clostridium difficile. Over the past decade, incidence, severity, and costs associated with C. difficile infection (CDI) have increased dramatically. The primary risk factor for CDI is antibiotic treatment, which disrupts the resident gut microbiota and leads to susceptibility to C. difficile. Interestingly, non-antibiotic associated CDI cases are on the rise, suggesting that unexplored host, environmental, and microbiota factors likely influence CDI. We are interested in identifying these environmental factors and defining underlying mechanisms of microbiota disruption and modulation of disease.

The research in our laboratory draws from numerous fields including microbiology, immunology, microbial ecology, host-pathogen interactions, and microbiota research. Our strategy is to leverage the strengths of high throughput sequencing technologies with more mechanistic strategies involving bacterial genetics, mass spectrometry, and imaging. Trainees in the laboratory gain interdisciplinary training and are involved in translational studies at the interface of basic and clinical research.

Keywords: Clostridium difficile; Enterococcus; Gut microbiome; Host-pathogen interactions; Pathogen-microbiota interactions; Inflammatory Bowel Disease; Colorectal cancer.


B.S. (Microbiology), University of Massachusetts - Amherst, 2008
M.S. (Microbiology), University of Massachusetts - Amherst, 2009
Ph.D. (Microbiology & Immunology), University of Michigan, 2014

Specialty Certification

Postgraduate Training

Postdoctoral Research Fellow, Vanderbilt University Medical Center, Nashville, TN, 2014-2018

Awards and Honors

Graduation with Honors, University of Massachusetts, 2008
Rackham Graduate School Travel Grant Award, 2012
Rackham Graduate Student Research Grant, 2012
Selected for ASM Live Research Highlight, May 2013, 2013
Rackham Graduate School Travel Grant Award, 2013
Vanderbilt Training Grant in Gastroenterology (NIH/NIDDK), 2014
F32 Ruth L. Kirschstein National Research Service Award Individual
Postdoctoral Fellowship (NIH/NIAID), 2015
Top Oral Presentation Award, 59th Annual Wind River Conference on
Prokaryotic Biology, 2015
Wind River Conference on Prokaryotic Biology Travel Award, 2015
Ward J. MacNeal Educational and Scientific Memorial Trust Distinguished
Dissertation Award, Department of Microbiology & Immunology, University
of Michigan, 2015
Top Abstract Award, Vanderbilt Postdoctoral Association and
Shared Resources Symposium, 2015
Top Abstract Award, 2015 Vanderbilt Institute of Chemical Biology Annual
Symposium, 2015
Best Poster Award, Microbiology and Immunology Division,
Vanderbilt Postdoctoral Association and Shared Resources Symposium, 2016
Top Poster Award, 2016 Vanderbilt Digestive Disease Research Center
Annual Symposium, 2016
Sidney P. Colowick Award for Outstanding Postdoctoral Research, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center., 2017
Selected as Postdoc Invited Speaker for Outstanding Research
Accomplishments, Annual Infection and Immunity Symposium, Vanderbilt
University Medical Center, 2017
Best Poster Award, Immunology and Infection Division,
Vanderbilt Postdoctoral Association and Shared Resources Symposium., 2017
CHOP Internal Nomination for Pew Biomedical Scholars, 2019
NIH Loan Repayment Program Award (NIH/NIAID), 2019
R13 NIH Early Career Scientist Travel Grant Awardee (NIH), Clostpath 11, 2019
K22 Career Transition Award (NIH/NIAID), 2019
2020 Award for Excellence in Mentoring Research Trainees, Children's Hospital of Philadelphia, 2020
CHOP Internal nomination for Mallinckrodt Scholars Award, 2020
Maximizing Investigator Research Award (NIH/NIGMS), 2020-2025

Memberships and Professional Organizations

American Society for Microbiology, 2008 - Present
Anaerobe Society of the Americas, 2015 - Present
National Mouse Metabolic Phenotyping Center MICROMouse Program, 2018 - 2018
Eastern Pennsylvania American Society for Microbiology Chapter, 2018 - Present
American Society for Microbiology, 2019 - 2019
Study Section (NIH) Antibacterial Drug Discovery or Resistance (DDR), 2021 - Present
Center for Molecular Studies in Digestive and Liver Diseases, 2021 - Present
PennCHOP Microbiome Program Advisory Board, 2021 - Present

Web Links

Selected Publications

Enterococci enhance Clostridioides difficile pathogenesis

Smith A.B., Jenior M.L., Keenan O., Hart J.L., Specker J, Abbas A, Rangel P.C., Di C., Green J., Bustin K. A., Gaddy J.A., Nicholson M.R., Laut C., Kelly B.J., Matthews M.L, Evans D.L., Van Tyne D., Furth E.E., Papin J.A., Bushman F.D., Erlichman J., Baldassano R.N., Silverman M.A., Dunny G.M., Prentice B.M., Skaar E.P., and Zackular J.P., Nature, 2022, PMID:36385534

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Investigation of Microbial Cooperation via Imaging Mass Spectrometry Analysis of Bacterial Colonies Grown on Agar and in Tissue During Infection

Specker J.T., Smith A.B., Zackular J.P., and Prentice B.M.., Journal of Visualized Experiments, 2022

Microbe-microbe Interactions During Clostridioides difficile Infection

Abbas A. and Zackular J.P., Current Opinions in Microbiology 53(): 19–25, 2020, PMID:32088581

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From Nursery to Nursing House: Emerging Concepts in Clostridioides difficile Pathogenesis.

Smith A.B., Soto Ocana J., and Zackular J.P., Infection and Immunity, 2020, PMID:32122939

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Nonsteroidal anti-inflammatory drugs alter the microbiota and exacerbate Clostridium difficile colitis while dysregulating the inflammatory response.

Maseda D.*, Zackular J.P.*, Trindade B., Kirk L., Crofford L.J., Schloss P.D., Roxas J.L., Viswanathan V.K., Vedantam G., Rogers L.M., Washington M.K., Skaar E.P., and Aronoff D.M., MBio 10(1): e02282-18, 2019, PMID:30622186

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Heme sensing and detoxification by HatRT contributes to pathogenesis during C. difficile infection.

Knippel R.J., Zackular J.P., Moore J.L., Celis A.I., Weiss A., Washington M.K., DuBois J.L., Caprioli R.M., and Skaar E.P., PLoS Pathogens 14(12): e1007486, 2018, PMID:30576368

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Dietary manganese promotes staphylococcal infection of the heart

Juttukonda L.J., Berends E.T.M, Zackular J.P., Stier M.T., Moore J.L., Zhang Y, Schmitz J.E., Beavers W.N., Wijers C.D., Kehl-Fie T, Atkinson J, Peebels R.S., Torres V.J., Caprioli R.M.,Skaar E.P., Cell Host and Microbe 22(): 1-12, 2017, PMID:28943329

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Dietary Zinc Alters the Microbiota and Decreases Resistance to Clostridium Difficile Infection

Zackular J.P., Moore J.L., Jordan A.T., Juttukonda L.J., Noto M.J., Nicholson M.R., Crews J.D., Semler M.W., Zhang Y., Ware L.B., Washington M.K., Chazin W.J., Caprioli R.M., Skaar E.P., Nature Medicine 22(11): 1330-34, 2016, PMID:27668938

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