Princeton, NJ 08544
In addition to the de novo production of small molecules, the human gut microbiome encodes a large repertoire of biochemical enzymes that can metabolize exogenous small molecules – whether they are derived from the human host, or from dietary or therapeutic sources. This concept has been explored for decades by using single isolates of the human microbiome against a common set of human-, drug-, or diet-derived chemicals, but has not been explored systematically. We aim to expand this area of research by developing high-throughout, unbiased approaches for defining the space of biochemical transformations that can be exerted by the collective human gut microbiome against a wide variety of chemicals, and the pharmacological consequences of these transformations.
Dr. Donia received his B.Sc in Pharmacy from the Faculty of Pharmacy, Suez Canal University, Egypt in 2004. He moved to the US in 2005 to study for his Ph.D. at the Medicinal Chemistry Department, School of Pharmacy, University of Utah. He worked in Dr. Eric Schmidt’s laboratory where he studied the chemistry and biology of small molecules produced by bacterial symbionts of marine animals. He used chemical, microbiological, and metagenomic techniques to study the role of small molecules in mediating microbe-host and microbe-microbe interactions in marine invertebrates. In 2010, he joined Dr. Michael Fischbach’s laboratory at the Department of Bioengineering and Therapeutic Sciences at the University of California, San Francisco. There, he studied small molecules produced by members of the human microbiome and their role in mediating microbe-host and microbe-microbe interactions in humans. In particular, he focused on antibiotics produced by human pathogens and commensals, and their role in shaping the composition and dynamics of the human vaginal and oral microbiota. Dr. Donia is a recipient of the NIH Director’s New Innovator Award, the Kenneth Rainin Foundation Innovation and Breakthrough Awards, and is named a Pew Biomedical Scholar. Dr. Donia is a member of the Scientific Advisory Board for Deepbiome Therapeutics.
|Jaime Lopez (Graduate Student)||Post-doc, Stanford University|
|Mary Davis (Undergraduate Student ’22)|
|Christian Hernandez (Undergraduate Student ’22)|
|Anna Schmedel (Faculty Assistant)|
|Shuo Wang (PhD Graduate Student)|
|Amira Mira (Postdoctoral Research Fellow)||Assistant Professor, Mansoura University, Egypt|
|Janie Kim (Princeton Undergrad ’21)||Graduate Student, Stanford University|
|Nisha Chandra (Princeton Undergrad ’21)|
|Jared Balaich (PhD Graduate Student)|
|Bahar Javdan (MD-PhD Graduate Student)|
|Amir Erez (Post-doc)|
|Dani Peters (Princeton Undergrad ’20)|
|Francine Camacho (PhD Graduate Student)||Viome|
|Yuki Sugimoto (Post-doc)|
|Zhiyuan Li (Post-doc)||Assistant Professor, Peking University|
|David Romero (Undergrad SURP Intern)||Undergrad, California State University, Northridge (CSUN)|
|Evan Zhao (Visiting Post-doc)||Post-doc, Massachusetts Institute of Technology|
|Lucy Williamson (Princeton Undergrad ’19)|
|Pranatchareeya Chankhamjon (Post-doc)||Scientist, VL55, Flagship Pioneering|
|Maria Diarey Tianero (Post-doc)||Senior Scientist (Program Lead), Lodo Therapeutics|
|Mohamed Farag (Visiting Associate Professor)||Associate Professor, Cairo University|
|Allison Chang (Princeton Undergrad ’18)||Masters Student, Computer Science, Princeton University|
|Diana Chin (Princeton Undergrad ’18)||Post-bac, Yu lab, Boston Children’s Hospital|
|Anna Posfai (Post-doc)||Post-Doc, Kinney lab, Cold Spring Harbor Laboratory|
|Tanya Tafolla (Summer Undergrad Intern)||Grad Student, University of California, Merced|
|Jindong Zan (Post-doc)||Staff Scientist, Becton Dickinson|
|Arman Odabas (Princeton Undergrad ’17)||Med Student, Washington University in St. Louis|
|Audrey Abend (Princeton Undergrad ’17)||Clinical Research Associate II, OpenBiome|
|Raphaella Hull (Oxford-Princeton Exchange Student)||Grad Student, University of Cambridge|
|Phoebe Huang (Princeton Undergrad ’16)||Med Student, University of Rochester|
|Christian Shema Mugisha (Summer Undergrad Intern)||Grad Student, Washington University in St. Louis|
MetaBGC is a computational algorithm that discovers small-molecule BGCs directly in complex metagenomic sequencing data of the human microbiome.
To download MetaBGC, please visit our GitHub.
For more information about MetaBGC, please refer to our paper: Sugimoto, Y.*, Camacho, F.R.*, et al. (2019) “A metagenomic strategy for harnessing the chemical repertoire of the human microbiome”. Science. 366 (6471): eaax9176.