Christopher Smillie, Ph.D.

Year of Graduation: 



Prof. Eric Alm

Current Position: 

Assistant Professor, Harvard Medical School; Principal Investigator, Massachusetts General Hospital

Smillie Lab Website


Doctoral Thesis Title:  Computational insights into the ecology of the human microbiota

Publications while at MIT: 

1.Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria.

Gomes ALC, Johns NI, Yang A, Velez-Cortes F, Smillie CS, Smith MB, Alm EJ, Wang HH.ISME J. 2020 Sep;14(9):2347-2357. doi: 10.1038/s41396-020-0696-1. Epub 2020 Jun 8.PMID: 32514119 Free PMC article.


2. Metagenomic mining of regulatory elements enables programmable species-selective gene expression.

Johns NI, Gomes ALC, Yim SS, Yang A, Blazejewski T, Smillie CS, Smith MB, Alm EJ, Kosuri S, Wang HH.Nat Methods. 2018 May;15(5):323-329. doi: 10.1038/nmeth.4633. Epub 2018 Mar 19.PMID: 30052624 Free PMC article.


3. Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation.

Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, Hohmann EL, Staley C, Khoruts A, Sadowsky MJ, Allegretti JR, Smith MB, Xavier RJ, Alm EJ.Cell Host Microbe. 2018 Feb 14;23(2):229-240.e5. doi: 10.1016/j.chom.2018.01.003.PMID: 29447696 Free PMC article.

4. Microbial reprogramming inhibits Western diet-associated obesity.

Poutahidis T, Kleinewietfeld M, Smillie C, Levkovich T, Perrotta A, Bhela S, Varian BJ, Ibrahim YM, Lakritz JR, Kearney SM, Chatzigiagkos A, Hafler DA, Alm EJ, Erdman SE.PLoS One. 2013 Jul 10;8(7):e68596. doi: 10.1371/journal.pone.0068596. Print 2013.PMID: 23874682 Free PMC article.


5. Probiotic bacteria induce a 'glow of health'.

Levkovich T, Poutahidis T, Smillie C, Varian BJ, Ibrahim YM, Lakritz JR, Alm EJ, Erdman SE.PLoS One. 2013;8(1):e53867. doi: 10.1371/journal.pone.0053867. Epub 2013 Jan 16.PMID: 23342023 Free PMC article.


6. Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease.

Papa E, Docktor M, Smillie C, Weber S, Preheim SP, Gevers D, Giannoukos G, Ciulla D, Tabbaa D, Ingram J, Schauer DB, Ward DV, Korzenik JR, Xavier RJ, Bousvaros A, Alm EJ.PLoS One. 2012;7(6):e39242. doi: 10.1371/journal.pone.0039242. Epub 2012 Jun 29.PMID: 22768065 Free PMC article.


7. Structure, function and diversity of the healthy human microbiome.

Human Microbiome Project Consortium.Nature. 2012 Jun 13;486(7402):207-14. doi: 10.1038/nature11234.PMID: 22699609 Free PMC article.