Daniel P. Beiting, Ph.D.

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Contact information
University of Pennsylvania
School of Veterinary Medicine
Department of Pathobiology
Rm 314 Hill Pavilion
380 S. University Avenue
Philadelphia, PA 19104-4539
Office: 2158989247
Lab: 2158989247
Ph.D. (Immunology)
Cornell University, 2006.
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Description of Research Expertise

The Beiting lab takes an interdisciplinary approach – leveraging immunology, genomics, publicly-available datasets, bioinformatics, and animal models – to identify mechanisms by which the microbiome influences infection and inflammation at barrier surfaces.

Our lab operates with an 'open science' philosophy, and has developed tools and methods that help the research community access, analyze, and visualize complex metagenomic datasets. The lab developed and runs an in-person and online course that teaches students how to use the R programming language to interrogate complex transcriptome and metatranscriptome studies. The Beiting lab also leads the MicrobiomeDB project, a web-based systems biology platform that integrates large, publicly-available microbiome studies and provides users with tools for analyzing and visualizing their own data.

- Microbiome
- Bioinformatics
- Host-pathogen interactions

Selected Publications

Berry ASF, Farias Amorim C, Berry CL, Syrett CM, English ED, Beiting DP.: An Open-Source Toolkit To Expand Bioinformatics Training in Infectious Diseases. mBio 12: e0121421, Aug 2021.

Berry ASF, Pierdon MK, Misic AM, Sullivan MC, O'Brien K, Chen Y, Murray SJ, Ramharack LA, Baldassano RN, Parsons TD, Beiting DP.: Remodeling of the maternal gut microbiome during pregnancy is shaped by parity. Microbiome 9: 146, Jun 2021.

Berry ASF, Johnson K, Martins R, Sullivan MC, Farias Amorim C, Putre A, Scott A, Wang S, Lindsay B, Baldassano RN, Nolan TJ, Beiting DP.: Natural Infection with Giardia Is Associated with Altered Community Structure of the Human and Canine Gut Microbiome. mSphere 5: e00670-20, Aug 2020.

Wang S, Martins R, Sullivan MC, Friedman ES, Misic AM, El-Fahmawi A, De Martinis ECP, O'Brien K, Chen Y, Bradley C, Zhang G, Berry ASF, Hunter CA, Baldassano RN, Rondeau MP, Beiting DP.: Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids. Microbiome 7: 126, Aug 2019.

Amorim CF, Novais FO, Nguyen BT, Misic AM, Carvalho LP, Carvalho EM, Beiting DP, Scott P.: Variable gene expression and parasite load predict treatment outcome in cutaneous leishmaniasis. Sci Transl Med 11: eaax4204, Nov 2019.

Wang S, El-Fahmawi A, Christian DA, Fang Q, Radaelli E, Chen L, Sullivan MC, Misic AM, Ellringer JA, Zhu XQ, Winter SE, Hunter CA, Beiting DP.: Infection-Induced Intestinal Dysbiosis Is Mediated by Macrophage Activation and Nitrate Production. mBio 10: e00935-19, May 2019.

Wilmore JR, Gaudette BT, Gomez Atria D, Hashemi T, Jones DD, Gardner CA, Cole SD, Misic AM, Beiting DP, Allman D.: Commensal Microbes Induce Serum IgA Responses that Protect against Polymicrobial Sepsis. Cell Host Microbe 23: 302-311, Mar 2018.

Oliveira FS, Brestelli J, Cade S, Zheng J, Iodice J, Fischer S, Aurrecoechea C, Kissinger JC, Brunk BP, Stoeckert CJ Jr, Fernandes GR, Roos DS, Beiting DP.: MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. Nucleic Acids Res 46: D684-D691, Jan 2018.

Gimblet C, Meisel JS, Loesche MA, Cole SD, Horwinski J, Novais FO, Misic AM, Bradley CW, Beiting DP, Rankin SC, Carvalho LP, Carvalho EM, Scott P, Grice EA.: Cutaneous Leishmaniasis Induces a Transmissible Dysbiotic Skin Microbiota that Promotes Skin Inflammation. Cell Host Microbe 22: 13-24, Jul 2017.

Misic AM, Cain CL, Morris DO, Rankin SC, Beiting DP.: Divergent Isoprenoid Biosynthesis Pathways in Staphylococcus Species Constitute a Drug Target for Treating Infections in Companion Animals. mSphere 1: e00258-16, Sep 2016.

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Last updated: 01/05/2023
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