Experience
November 2019 - Present: Consultant for OpenBiome
OpenBiome is a non-profit stool bank and microbiome research institute. As a consultant for OpenBiome, I have helped them develop a framework for launching new research initiatives, performed a landscape analysis to help them prioritize indications for these new initiatives, developed a cost-benefit analysis for their stool donor screening program, and assisted them with writing and publishing the results of these analyses.
March 2019 - July 2020: Consultant for Finch Therapeutics
Finch Therapeutics is a microbiome biotech start-up. Asa consultant for Finch. I evaluate potential partners and collaborators as well as new indications and technologies to inform Finch R&D strategy.
January 2018 - March 2019: Program Development Manager at Finch Therapeutics
As a member of the program development team, I worked on projects that established the strategic direction for new Finch programs and platforms. These projects involved working with the commercial and clinical teams to perform detailed analyses that could inform Finch’s R&D strategy. I also worked with the research, clinical, and product development team leadership to create plans that will lead to first-in-class or best-in-class microbiome therapeutics. I also evaluated potential academic collaborators, industry partners, and contract research organizations for their ability to execute on these research plans; and I managed some of these partnerships/collaborations. In this role, I assisted in launching Finch’s autism and oncology programs and led an important initiative to better understand how dose and regimen influence different pharmacokinetic and pharmacodynamic markers.
July 2016 - December 2017: Research Scientist at Finch Therapeutics
As part of this position, I worked on bioinformatics projects, performed wet lab research, and led a project to assess the feasibility of a new Finch program. I developed a microbiome disruption index that could be used to classify patients who had Clostridium difficile infection and predict which patients were likely to develop bloodstream infection; I managed four research associates on the microbiology team and the three different projects they were moving forward; and I developed a plan to research and develop a microbiome therapeutic to treat urinary tract infections and presented it to the Finch Board of Directors.
Education
May 2016: Ph.D. in Chemical Biology, Harvard University
I adapted a high-frequency transposition system for compatibility with next-generation sequencing to create high-density transposon libraries in methicillin-resistant Staphylococcus aureus (MRSA) strains. I treated these libraries with antibiotics, which allowed us to identify new intrinsic antibiotic resistance factors. I have also developed a way to use this data to train a machine learning algorithm that could then predict the mechanism of action for new antibiotics. This work will enable new strategies for treating antibiotic resistant infections.
May 2010: B.S. in Molecular Biophysics and Biochemistry, Yale University
Publications
M Santiago et al. A framework for prioritizing therapeutic research in fecal microbiota transplantation. 2020; Manuscript in preparation for submission to PLoS Biology.
M Santiago and Olesen SW. 16S sequencing of samples from universal stool bank donors. 2020; Manuscript in preparation for submission to BMC Research Notes
Schaefer K, Owens TW, Page JE, Santiago M, Kahne D, Walker S. Structure and reconstitution of a hydrolase complex that releases peptidoglycan from the membrane after polymerization. Accepted in Nature Microbiology 2020. https://www.biorxiv.org/content/10.1101/2020.05.21.109470v1
Kang D, Adams JB, Vargason T, Santiago M, Hahn J, Krajmalnik-Brown R. Distinct fecal and plasma metabolites in children with autism spectrum disorders and their modulation after microbiota transfer therapy. mSphere 2020;5(5):e00314-20. DOI: 10.1128/mSphere.00314-20
Schuster CM, Wiedemann DM, Kirsebom FCM, Santiago M, Walker, S, and Grundling A. High-throughput transposon sequencing highlights the cell wall as an important barrier for osmotic stress in methicillin resistant Staphylococcus aureus and underlines a tailored response to different osmotic stressors. Molecular Microbiology 2019;113:699-717. DOI: 10.1111/mmi.14433
Santiago M et al. Microbiome predictors of dysbiosis and VRE decolonization in patients with recurrent C. difficile infections in a multi-center retrospective study. AIMS Microbiology. 2019 Jan;5(1):1-18. DOI: 10.3934/microbiol.2019.1.1
Santiago M et al. Genome-wide mutant profiling predicts the mechanism of a Lipid II binding antibiotic. Nature Chemical Biology 2018 Jun;14(6):601-608. DOI: 10.1038/s41589-018-0041-4
Santiago M and Wong W. Microbial approaches for targeting antibiotic resistant bacteria. Microbial Biotechnology 2017 Sep;10(5):1047-1053. DOI: 10.1111/1751-7915.12783
Santiago M et al. Multidrug Intrinsic Resistance Factors in Staphylococcus aureus Identified by Profiling Fitness within High-Diversity Transposon Libraries. MBio 2016 Aug 16;7(4). DOI: 10.1128/mBio.00950-16
Pasquina L, Santa Maria JP, Wood BM, Moussa SH, Matano L, Santiago M, Martin SES, Lee W, Meredith TC, and Walker S. A synthetic lethal approach for compound and target identification in Staphylococcus aureus. Nature Chemical Biology 2016 Jan;12(1):40-45. DOI: 10.1038/nchembio.1967
Santiago M et al. A new platform for ultra-high density Staphylococcus aureus transposon libraries. BMC Genomics 2015 Mar 29;16(1):252. DOI: 10.1186/s12864-015-1361-3
Santiago M and Strobel S. Thin Layer Chromatography. 2013 Methods in Enzymology 533:303-324. DOI: 10.1016/B978-0-12-420067-8.00024-6
Russell JR, Huang J, Anand P, Kucera K, Sandoval AG, Dantzler KW, Hickman D, Jee J, Kimovec FM, Koppstein D, Marks DH, Mittermiller P, Nunez SJ, Santiago M, Townes MA, Vishnevetsky M, Williams N, Vargas MPN, Boulanger L, Bascon-Slack C, Strobel SA. Biodegredation of polyester polyurethane by endophytic fungi. Applied Environmental Microbiology 2011 Sep:77(17):6076-6084. DOI: 10.1128/AEM.00521-11
Selected Presentations
June 2017: ASM Microbe, New Orleans, LA. Title: Development of a microbiome disruption index and its use in predicting infection.
March 2015: Spring National Meeting of the American Chemical Society, Denver, CO. Title: Investigating antibiotic resistance using high-density transposon libraries in MRSA.
March 2015: Museum of Science Health Fair, Boston, MA. Title: The human microbiome and antibiotic resistance.
July 2014: Gordon Conference on Drug Resistance, Sunday River Resort, ME. Poster Title: Identification of cell envelope interactions in MRSA using a high efficiency transposition system. This presentation won the poster competition and was chosen for oral presentation.
July 2014: Boston Museum of Science Podcast, Boston, MA. Topic: Fighting Antibiotic Resistance http://www.mos.org/node/3331451
June 2014: Boston Bacteriological Meeting, Cambridge, MA. Poster Title: Identification of cell envelope interactions in MRSA using a high efficiency transposition system. This presentation won 2nd place in poster competition.
Selected Leadership Experience
August 2017 – Nov 2018: Founding Member of Finch/OpenBiome Mentorship Program Steering Committee
Spring 2015: Boston Manager of Voice of Young Science for Sense About Science
Fall 2013 – Fall 2014: President of Harvard Chemical Biology Graduate Student Organization
Fall 2012 – Fall 2013: Co-founder and Vice President of Harvard Chemical Biology Graduate Student Organization
Spring 2012 – Spring 2015: Member of Student Steering Committee for the Harvard Infectious Diseases Consortium at Harvard Medical School
Selected Teaching Experience
Spring 2018: Designed and led a two session Microbiome Drug Development Course for a diverse group of Finch employees
Fall 2017: Designed and led two python bootcamps for members of the Finch Microbiology team
Spring 2015: Teaching Fellow, Social Issues in Biology, Harvard University
Fall 2014: Head Teaching Fellow, Science and Cooking, Harvard University