We currently host 7667 Microbes!

What we do

The Microbe Directory is a collective research effort to profile and annotate 7667 microbes, so that it may be used downstream of metagenomic taxonomic analyses. It does so by collecting data on various microbe characteristics, which allows one to link simple taxonomic classifications to more interesting parameters. Such characteristics include, but are not limited to: COGEM class risk rating, optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, and antimicrobial resistance; among others. The database has been curated by trained student-researchers from Weill Cornell Medicine and CUNY—Hunter College, and its analysis remains an ongoing effort in the Mason Laboratory.

In its current form, The Microbe Directory is a SQL database that can be queried for the aforementioned parameters by a microbe’s taxonomy. In many metagenomic analyses, an environmental sample is processed for the DNA it contains and the microbes present in the sample are reported. Many such taxonomic analyses stop at this stage, but The Microbe Directory allows this to be taken one step further. Instead of simply reporting the microbes present, one could use The Microbe Directory to analyze the sample by optimal growth pH of the microbes living there (or by any other parameter in the database). Such a curated database allows one to explore novel properties about the microbial DNA present in the metagenomic sample. The Microbe Directory will also provide a common platform for storage, retrieval, and analysis into which other microbial database projects could be incorporated. It is the largest and most comprehensive curated database on microbial species.


Who we are

Project Lead

Christopher Mason, PhD
Heba Shaaban
David Westfall
David Danko
Rawhi Mohammad

Other Researchers

Sophie Dornbaum - Weill Cornell Medicine
Rabab Shaddoud - CUNY Hunter College
Sadia Chowdhury - CUNY Hunter College
Sarah Chebli - CUNY Hunter College
Christopher Chiang - CUNY Hunter College
Ellen Koag - CUNY Hunter College
Sophia Tam - CUNY Hunter College
Christopher Campbell - CUNY Hunter College
Timothy Lau - CUNY Hunter College
Camille Derderian - CUNY Hunter College
Elyas Amin - CUNY Hunter College
Nicole Rakhmanova - CUNY Hunter College
Amina Durakovic - CUNY Hunter College
Jereen Chowdhury - CUNY Hunter College
Catherine Ng - CUNY Hunter College
Jasmine Wong - CUNY Hunter College
Phuong Vo - CUNY Hunter College
Calvin Herman - CUNY Hunter College
Silva Baburyan - CUNY Hunter College
Kevin Londono - CUNY Hunter College
Julianna Romeo - CUNY Hunter College
Leah Katz - CUNY Hunter College
Valentina Bedoya - CUNY Hunter College
Juan Cambeiro - CUNY Hunter College
Amzad Chowdhury - CUNY Hunter College
Rangon Islam - CUNY Hunter College
Bibi Begum - CUNY Hunter College
Frances Chung - CUNY Hunter College
Naveed Shah - Adelphi University
Phillip Ye - CUNY Hunter College
Madeleine Winter - Poly Prep High School
Kriti Devasenapathy - California Institute of Technology
Raghav Pant - Millburn High School
Halime Sena Bastug - Istanbul University Cerrahpasa Medical Faculty
Chou Chou - Weill Cornell Medicine
Jasmine Sharron - Columbia Secondary School
Laolu Ogunnaike - Johns Hopkins University
Alina Sheikh - Adelphi University
Carol Apai - Rutgers New Jersey Medical School
Salama Chaker - Weill Cornell Medicine Qatar
Caleb Gordon - Bowdoin College
Michael Pineda - Arizona State
Dara Pierre - CUNY John Jay
Scott Kulm - Cooper Union
Ike Lewis - Weill Cornell Medicine
Mustafa Hakyemezoglu - Weill Cornell Medicine


Support Us

Help support The Microbe Directory here!

Alternatively, donations can be mailed to:
Weill Cornell Medical College
Office of External Affairs
1300 York Avenue, Box 314
New York, NY 10065
Phone: 646-317-7427 or toll free: 866-329-8915

Checks should be payable to “Weill Cornell Medical College” and donors should indicate “The Microbe Directory” on the notation line of the check.

Weill Cornell Medical College’s Office of External Affairs will issue tax receipts to all donors.

Money donated to the The Microbe Directory project will go towards paying for consistent updating of the database and website, funding student volunteers working on the project, and expanding the project’s aims.