Faculty

Ahmed M Moustafa, PhD

Assistant Professor of Pediatrics (Gastroenterology, Hepatology and Nutrition) at the Children's Hospital of Philadelphia

Department: Pediatrics

Graduate Group Affiliations

Contact information

Children's Hospital of Philadelphia
Abramson Pediatric Research Center
3615 Civic Center Boulevard Room 902C
Philadelphia, PA 19104

Lab: 2155909987

Email:
moustafaam@chop.edu

Publications

Search PubMed for articles

Education:
BPharm (Pharmaceutical Sciences)
Alexandria University, Alexandria, Egypt, 2009.
Ph.D. (Biomedical Sciences)
Murdoch University, Perth, Australia, 2015.
Cert (Research Mentor Training: Effective Communication and Aligning Expectations.)
PSOM ITMAT, 2022.

Links
Search PubMed for articles
The Sequencing Core provides expertise in next-generation sequencing of microbiome samples and single microbial isolates.
Github account where I maintain the bioinformatics tools I develop
Google Scholar Account

Permanent link

> Perelman School of Medicine > Faculty > Details

Description of Other Expertise

SARS-CoV-2 Genomics and Evolution

Description of Research Expertise

Dr. Moustafa is currently the Director for the CHOP Microbiome Sequencing Core and the Co-Director for the microbial ARchive and Cryo-collection (mARC) unit under the PennCHOP Microbiome program. Dr. Moustafa’s research program focuses on evolutionary microbiology, microbial genomics and infectious diseases. The overall goals of the Moustafa laboratory are to 1) build a highly curated strain library of pathogenic and commensal microbes to fuel microbial genomics research and microbiome mechanistic studies 2) pinpoint the molecular determinants of infectious diseases using big genomics data and novel bioinformatics tools 3) bring the tools of next-generation sequencing and microbial genomics to biologists and clinicians using innovative educational approaches.
Keywords: Microbial Genomics; Bioinformatics; microbiome; Population Genetics; Phylogenetics; Bacterial Pathogenesis.

Selected Publications

Johanna M.S. Lemons, Adrienne B. Narrowe, Jenni Firrman, Karley K. Mahalak, LinShu Liu, Higgins S, Moustafa AM, Aurélien Baudot, Stef Deyaert, Pieter Van den Abbeele: The food additive butylated hydroxyanisole minimally affects the human gut microbiome ex vivo. Food Chemistry 473, May 2025.

Martínez JRW, Alcalde-Rico M, Jara-Videla E, Reyes J, Carvajal LP, Rincon S, Ríos R, Diaz L, Quesille-Villalobos A, Riquelme-Neira R, Rivas L, Moustafa AM, Hanson B, Undurraga EA, Olivares-Pacheco J, García P, Araos R, Planet PJ, Arias CA, Munita JM.: Geographic divergence of methicillin-resistant Staphylococcus aureus ST5-SCCmecI in the aftermath of a major earthquake and tsunami: impact of a plasmid harboring heavy metal resistance genes. mBio Mar 2025.

Liu S, Rodriguez J, Munteanu V, Ronkowski C, Sharma N, Alser M, Andreace F, Blekhman R, Błaszczyk D, Chikhi R, Crandall K, Della Libera K, Francis D, Frolova A, Gancz A, Huntley N, Jaiswal P, Kosciolek T, Łabaj P, Łabaj W, Luan T, Mason C, Moustafa AM, Muralidharan H, Mutlu O, Ghiasi N, Rahnavard A, Sun F, Tian S, Tierney B, Van Syoc E, Vicedomini R, Zackular J, Zelikovsky A, Zielińska K, Ganda E, Davenport E (R), Pop M, Koslicki D, Mangul S.: Analysis of metagenomic data. Nature Reviews Methods Primers 5, Jan 2025.

Zirbes CF, Feder A, Pamatmat AJ, Bartels AR, Pitcher NJ, Rozen AL, Teresi M, Krogh J, Regan M, Arnold EA, Hill JJ, Reinhardt LD, Oberto CL, Boyken L, Reeb VC, Moustafa AM, Planet PJ, Fischer AJ. : Genetic Concordance of Staphylococcus aureus From Oropharyngeal and Sputum Cultures in People with Cystic Fibrosis. Pediatric Pulmonology Jan 2025.

Mulcrone PL, Narrowe A, Jones S, Hu W, Bittinger K, Moustafa AM, Firrman, J. : Monitoring the impact of chlorinated drinking water on the developing gut microbiota of adolescent mice using genetic profiling. International Journal of Environmental Studies Page: 1-18, Jan 2025.

Alameh MG, Semon A, Bayard NU, Pan YG, Knox J, Dwivedi G, Glover RC, Rangel PC, Tanes C, Bittinger K, She Q, Maslanka JR, Planet PJ, Moustafa AM, Davis B, Chevrier A, Beattie M, Ni H, Blizard G, Furth EE, Mach RH, Lavertu M, Sellmyer M, Tam Y, Abt MC, Weissman D, Zackular JP. : A multivalent mRNA-LNP vaccine protects against Clostridioides difficile infection. Science 386(6717): 69-75, Oct 2024.

Yamana TK, Rajagopal S, Hall DC Jr., Moustafa AM, Feder A, Ahmed A, Bianco C, Harris R, Coffin S, Campbell AE, Pei S, Mell JC, Planet PJ, Shaman J.: A two-variant model of SARS-COV-2 transmission: Estimating the characteristics of a newly emerging strain. BMC Infectious Diseases 24, Sep 2024.

Urso A, Monk I, Predella C, Fok Lung TW, Theiller E, Boylan J, Perelman S, Baskota S, Moustafa AM, Lewis I, Torres V, Chen YT, Lohia GK, Howden B, Stinear T, Dorrello NV, Prince A.: Staphylococcus aureus adapts to exploit collagen-derived proline during chronic infection. Nature Microbiology 9: 2506–2521, Aug 2024.

Mahalak KK, Liu L, Bobokalanov J, Narrowe A, Firrman J, Bittinger K, Hu W, Jones S and Moustafa AM: Supplementation with soluble or insoluble rice-bran fibers increases short-chain fatty acid producing bacteria in the gut microbiota in vitro. Front. Nutr. Sec. Nutrition and Microbes. Frontiers, 11, May 2024.

Liu L, Mahalak KK, Bobokalonov JT, Narrowe AB, Firrman J, Lemons JMS, Bittinger K, Hu W, Jones SM, Moustafa AM.: Impact of Ivermectin on the Gut Microbial Ecosystem. International Journal of Molecular Sciences. International Journal of Molecular Sciences, 24(22), November 2023.