Ahmed M Moustafa, PhD
Assistant Professor of Pediatrics (Gastroenterology, Hepatology and Nutrition) at the Children's Hospital of Philadelphia
Co-Director, Microbial ARchive and Cryo-Collection (mARC), Children's Hospital of Philadelphia, University of Pennsylvania
Director, Microbiome Sequencing Core, Children's Hospital of Philadelphia, University of Pennsylvania
Co-Director, Center for Microbial Medicine, Children's Hospital of Philadelphia, University of Pennsylvania
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
Abramson Pediatric Research Center
3615 Civic Center Boulevard Room 902C
Philadelphia, PA 19104
Lab: 2155909987
Email:
moustafaam@chop.edu
moustafaam@chop.edu
Publications
Links
Search PubMed for articles
The Sequencing Core provides expertise in next-generation sequencing of microbiome samples and single microbial isolates.
Co-Director for the Center for Microbial Medicine, a Center of Emphasis established at CHOP in August 2024.
Google Scholar Account
Github account where I maintain the bioinformatics tools I develop
Executive Leadership for the Microbiome Centers Consortium
Search PubMed for articles
The Sequencing Core provides expertise in next-generation sequencing of microbiome samples and single microbial isolates.
Co-Director for the Center for Microbial Medicine, a Center of Emphasis established at CHOP in August 2024.
Google Scholar Account
Github account where I maintain the bioinformatics tools I develop
Executive Leadership for the Microbiome Centers Consortium
Education:
BPharm (Pharmaceutical Sciences)
Alexandria University, Alexandria, Egypt, 2009.
Ph.D. (Biomedical Sciences)
Murdoch University, Perth, Australia, 2015.
Permanent linkBPharm (Pharmaceutical Sciences)
Alexandria University, Alexandria, Egypt, 2009.
Ph.D. (Biomedical Sciences)
Murdoch University, Perth, Australia, 2015.
Description of Other Expertise
SARS-CoV-2 Genomics and EvolutionDescription of Research Expertise
Dr. Moustafa is currently a Co-Director for the Center for Microbial Medcine at CHOP and the Director for the CHOP Microbiome Sequencing Core 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
McGann C, Strysko J, Bayani O, Moorad B, Ntlhako N, Nwako N, Hu W, Tanes C, Moustafa AM, Jones SM, Nakstad B, Gezmu AM, Arscott-Mills T, Goldfarb DM, Steenhoff AP, Richard-Greenblatt M, Machiya T, Thela T, Mokomane M, Paganotti GM, Vurayai M, Zalot M, Boustany M, Planet PJ, Coffin S, Bittinger K: Effect of maternal HIV status on the early neonatal microbiome. Journal of the Pediatric Infectious Diseases Society 14(10): piaf076, October 2025 Notes: https://doi.org/10.1093/jpids/piaf076.Liu L, Lemons JMS, Firrman J, Mahalak KK, Chetty VJ, Narrowe AB, Higgins S, Moustafa AM, Baudot A, Deyaert S, Van den Abbeele P: Hydrogen Sulfide Has a Minor Impact on Human Gut Microbiota Across Age Groups. Sci 7(3): 102, August 2025 Notes: https://doi.org/10.3390/sci7030102.
Theiller E, Galis BE, Jones S, Napper T, She Q, Srinivasan L, Zackular JP, Planet PJ, Moustafa AM: Unraveling the Epidemiological Dynamics of Staphylococcus epidermidis in Pediatric Bacteremia. GRS Staphylococcal Diseases Conference, Barcelona, Spain, Podium August 2025.
Moustafa AM*, Theiller E, Lal A, Yamali S, Feder A, Narechania A, Planet PJ: Redcarpet: A Tool for Rapid Recombination Detection in Staphylococcus aureus and Other Species Amidst Expanding Genomic Databases. GRS Staphylococcal Diseases Conference, Barcelona, Spain, Poster August 2025.
Lemons JMS, Firrman J, Mahalak KK, Liu L, Narrowe AB, Higgins S, Moustafa AM, Baudot A, Deyaert S, Van den Abbeele P: The Effect of Sodium Benzoate on the Gut Microbiome Across Age Groups. Foods 14(17): 2949, August 2025 Notes: https://doi.org/10.3390/foods14172949.
L’Etoile NL, Sundararaman SA, Theiller E, Miller JJ, Moustafa AM, Steenhoff AP, Odom John AR: Pocapavir for neonatal enteroviral sepsis: limitations of rapid viral sequencing on treatment decisions. ASM Case Reports 1(6): e00008-25, July 2025 Notes: https://doi.org/10.1128/asmcr.00008-25.
Free M, Soper N, Slaughter JC, Feder A, Bianco C, Moustafa AM, Planet P, Creech CB, Thomsen I: Evolution of strain diversity and virulence factor repertoire in pediatric Staphylococcus aureus isolates. PLoS One 20(7): e0326353, July 2025 Notes: https://doi.org/10.1371/journal.pone.0326353.
Rotsaert C, Minnebo Y, Duysburgh C, Liu LS, Mahalak KK, Firman J, Mattei LM, Moustafa AM, Bittinger K, Hu W, Marzorati M, Michiels J, Van de Wiele T: Digestive parameters and gut microbiota load and composition along the in vivo piglet gastrointestinal tract. Journal of Animal Science 103(1): skaf107, May 2025 Notes: https://doi.org/10.1093/jas/skaf107.
Lemons JMS, Narrowe AB, Firrman J, Mahalak KK, Liu L, Higgins S, Moustafa AM, Baudot A, Deyaert S, Van den Abbeele P.: The food additive butylated hydroxyanisole minimally affects the human gut microbiome ex vivo. Food Chemistry 473(2): 143037, May 2025 Notes: https://doi.org/10.1016/j.foodchem.2025.143037.
Kelliher JM, Aljumaah M, Bordenstein SR, Brister JR, Chain PSG, Dundore-Arias JP, Emerson JB, Fernandes VMC, Flores R, Gonzalez A, Hansen ZA, Hatcher EL, Jackson SA, Kellogg CA, Madupu R, Miller CML, Mirzayi C, Moustafa AM, Mungall C, Oliver A, Pariente N, Pett-Ridge J, Record S, Reji L, Reysenbach A-L, Rich VI, Richardson L, Schriml LM, Shabman RS, Sierra MA, Sullivan MB, Sundaramurthy P, Thibault KM, Thompson LR, Tighe S, Vereen E, Eloe-Fadrosh EA.: Microbiome data management in action workshop: Atlanta, GA, USA, June 12–13, 2024 BMC Environmental Microbiome 20(1): 40, April 2025 Notes: https://doi.org/10.1186/s40793-025-00702-9.