Alumni

Thesis: Developing Nucleic Acid-Based Sensors and Actuators

Investigate the anti-virulence effects of mucin, natively purified from mucus, on microbial pathogens to better understand host-microbe dynamics.

Evaluate mucin’s ability to alter biofilm formation of opportunistic and drug-resistant pathogen Klebsiella pneumoniae. Presented to scientific audiences eight times on this independent project, including both posters and talks. First author publication in preparation.

Determine the mechanism by which mucin prevents Salmonella typhimurium virulence. First author publication in preparation.Investigate

Thesis: Mucin and mucin glycans alter behavior of mucosal pathogens.

I’m curious how microbes shape their environment across different scales of space and time. My research focuses on microbial biogeochemistry and evolution, especially pertaining to microbial nitrogen cycling. Before coming to MIT Microbiology, I studied bacterial evolution and marine sponge symbionts at UC San Diego and the Scripps Institution of Oceanography, and received my Master’s in Science Writing here at MIT; I also worked as a reporter and researcher at Science News in Washington, D.C. In addition to science and writing, I’m a fan of baking, hiking, musicals, and baseball.

Thesis: The evolution and diversity of noncanonical microbial nitrogen metabolisms

Thesis:  Directed Evolution of Glycan-Binding Proteins   

Thesis: Interactions between mobile genetic elements and their bacterial hosts

Thesis: High-resolution time series reveals differential behaviors of closely-related microbes in coastal communities.

Thesis: Tools for engineering multicellular systems through cell sorting and cell state detection.

I am mainly interested in scientific areas dealing with many-organisms questions, such as ecology, community assembly and population genetics. As an undergrad I worked with bacteria developing resistance to antibiotics and with bacteria growing inside the gut of C. elegans. So far, my plans for grad school are to measure as much as we can a specific bacterial community and see how that fits into our theoretical frameworks. Outside the lab, I cook, listen to music and play soccer and waterpolo. Cheers!

Thesis: Bacterial  Interspecies Interactions and Microbial Community Assembly

Thesis: Investigation of two-component signaling systems in Pseudomonas aeruginosa and their roles in the mucus barrier

Thesis: The influence of mucin glycans on microbial virulence and competition

• Thesis: Commensal-specific adaptive immune response at the intestinal mucosa
• All Publications

Biotech entrepreneur originally trained as a microbe engineer. Interested in bacterial products, microbiome science, and microbiome product development.
I spent my academic years engineering microbes for chemical production and studying how microbes can be naturally beneficial to their host. Through those academic years I developed two strong beliefs. The first one, is that humanity will greatly benefit from domesticating as many microbes as possible. The second one, is that it is a scientist’s duty to push their newly developed technologies out of academia and into industry.
If any of the above spark your interest, I’d love to hear your thoughts.Biotech

Thesis: Tool development for the rapid identification of microbiome manipulating agents

Caitlin Friend is a Digital Learning Lab Fellow postdoctoral associate for the Department of Biology and former Learning Technologist. She completed her PhD with her project entitled “The Roles of the Helicase Double-Hexamer Complex and the ssDNA-Binding Protein RPA During Eukaryotic DNA Replication” in Steve Bell’s lab at MIT. Since January 2020, Caitlin has been a core member of the MITx Biology course development team.

Thesis: The roles of the helicase double-hexamer complex and the ssDNA-binding protein RPA during eukaryotic DNA replication

Thesis: Effects of the Mobile Genetic Element ICEBs1 on the Bacterial Host Fitness

Thesis: Engineering Probiotic Microbes for In Vivo Applications

Thesis: Rapid nutrient fluctuations and their implications for bacterial growth.

Ben is a Postdoctoral Fellow in the Stanford Department of Microbiology and Immunology. Ben’s research focuses on host-pathogen interactions, with a particular focus on species-specific defense systems and viral antagonism of those systems. Ben received his PhD from MIT, where he studied the regulation of chronic infection by the parasite Toxoplasma gondii in Sebastian Lourido’s group at the Whitehead Institute.

Thesis: Identification of a master regulator of differentiation in Toxoplasma gondii

Thesis: Regulation of DNA replication and the replication initiator, DnaA, in Bacillus subtilis

A childhood spent chasing bugs set me up for a life working to avert ecological collapse. I am helping build Tezza (tezzafoods.com)—a public benefit corporation that discovers and designs microbial communities to transform inexpensive plants into new categories of sustainable fermented foods. We are starting with the most resource-intensive and addictive dairy product: cheese.

In past lives as a field, experimental, and computational biologist, I’ve studied the dynamics of complex systems, from coral disease to poop. As a facilitator, I’ve taught leadership workshops during multiweek kayaking expeditions.

If you share my mission of a more connected world, please let me know how I can help.

Thesis: Translating dynamics of human-microbe interactions

Thesis: Developing VHH-based tools to study Ebolavirus Infection

Thesis: The eco-evolutionary dynamics of microbial populations

Thesis: Development of natural and engineered bacteriophages as antimicrobials

Thesis: Characterization of influenza A virus evolution in laboratory hosts

Besides science, my passion is dancing. I dance different Colombian traditional folkloric rhythms. I participate in performances in which we showcase the culture, history and traditions of our country through folkloric dances. I also enjoy reading good books, science or non-science related. Also I have participated in public health campaigns to prevent transmission of tropical infectious diseases in Colombia, which is the ultimate goal that I expect to accomplish through my research and fieldwork. After graduate school, I am planning to pursue a career in the academia to continue my work in infectious diseases.

Alejandra Falla Castillo CV (PDF)

Thesis: Genome engineering andfunctional gene regulation tools for the study of malaria parasites

Thesis : Scalable platforms for computation and memory in living cells

Mark Mimee is an Assistant Professor in the Department of Microbiology and the Pritzker School of Molecular Engineering. His interest in microbial life began in Montreal, Canada, where he completed his Bachelor of Science in Microbiology & Immunology at McGill University. Inspired by the nascent field of synthetic biology, Mark pursued studies at the Massachusetts Institute of Technology, completing his PhD in Microbiology with Dr. Timothy Lu as an HHMI International Student Fellow and a Qualcomm Innovation Fellow. His research focuses on developing strategies to precisely engineer the activity and composition of the microbiota. His long-term vision is to implement these technologies to chart new basic and translational studies to exploit the microbiota for human health. Outside of the lab, Mark enjoys baking savoury pies, fermenting food and drink, playing double bass, and trying to stay in shape.

Thesis: Genetic technologies to engineer and understand the microbiome

Thesis: Horizontal gene transfer as a cohesive force in microbial populations

Thesis: Examining the effects of environmental compounds on influenza virus ecology

• Thesis: A deadly hug: contact-dependent killing by Caulobactor crescentus, via cell surface-associated glycine-zipper proteins
• Trust Your Gut: How This Colombian Scientist Found Her Field

• PhD in microbiology from MIT (2017)
• College professor for 5 years
• Areas of expertise: biotechnology, microbial ecology, infectious disease, technical writing, quantitative research & analysis, evidence-based methods for teaching & skills assessment, and DEI (diversity, equity & inclusion)

Thesis: Insights into microbial community structure from pairwise interaction networks

Thesis: Mechanism of Mcm10 Function during DNA replication

Biological problem solver who excels at analyzing, distilling, and communicating key findings from complex, high-throughput datasets. Unlocks discoveries with diverse laboratory and data processing skills.Biological

Thesis: Systematic determination of a transcription factor/binding site functional interaction landscape

Thesis : New mechanisms in transcription regulation and chromosome organization in Caulobacter crescentus

Dr. Diana Chien has worked with the MIT Communication Lab since its launch in 2013, and became program director in the spring of 2017, following the departure of founder Jaime Goldstein. From 2013-2015, Diana was a Biological Engineering (BE) Communication Fellow, while she was a PhD student in the Microbiology graduate program. From 2016-2017, she led the BE Communication Lab and taught the communication curricula for BE’s two communication-intensive undergraduate courses. During that time, she also led the launch of the Communication Lab’s suite of online resources, the CommKit, which she co-designed with BE Communication Fellow alumnus Dr. Scott Olesen.

Thesis : Fine-scale ecological dynamics of closely related marine microbes

Thesis : Rodent inflammasome activation by Toxoplasma gondii

Jacob (Jake) Rubens, Ph.D., joined Flagship Pioneering in 2015 and is a Senior Principal. He is a scientist, inventor, and entrepreneur, and works as part of a venture-creation team, founding and growing companies based on new biotechnology.

At Flagship, Jake co-founded Sana Biotechnology and Tessera Therapeutics, and launched Kaleido Biosciences. Jake is the Chief Innovation Officer and founding Chief Scientific Officer at Tessera, where he led research from 2018 through 2021. Previously, Jake was the Head of Innovation at Cobalt Biomedicine, where he co-invented and developed the company’s Fusosome platform prior to its merger with Sana Biotechnology.

• Thesis : Synthetic biological circuits for continuous signal processing
• 2017 Forbes 30 Under 30 List for Science

PhD molecular biologist with deep expertise in building products and scaling operations in early stage biotech startups and small teams. Experienced in working cross-functionally with Data Science, Software Engineering and BD teams. Areas of professional interest include lab automation, operational optimization, sustainability and food tech. Thrives in fast-paced, interdisciplinary team environments. Currently working on productionalization and scale up of enzyme assays at NEB.PhD

Thesis: Protein engineering and bioprospecting for selective hydroxyacid production in engineered Escherichia coli

Scientist turned strategist. Passionate about cutting edge science, ambiguous problems, and driving to decisions informed by data. Strong people developer with track record of creating high performing teams. 

Thesis : Toxin-antitoxin systems in bacteria: targets, mechanisms, & specificity

Life science researcher with expertise in mucosal and epithelial cell biology and microbiology/bacterial pathogenesis. Experienced in developing in vitro cell culture models, including human primary cell-derived 3D enteroid/organoid systems, and designing assays with which to characterize them. Enjoys collaborating with team members from different scientific backgrounds to develop creative solutions to challenging interdisciplinary problems. Passionate about designing tools and strategies for effective communication with diverse audiences. Life

Thesis : The influence of mucins onbacterial communities

Andrés is a Research Scientists at the Institute for Medical Engineering and Science at MIT. He is a microbiologist with expertise in synthetic biology and genomics. His work focuses the development of an engineered live biotherapeutic (eLBP) platform that targets the gut microbiota for the prevention and treatment of human diseases. As a visiting scholar in the Wyss Living Cellular Devices platform, Andrés has led a Wyss Validation Project aiming at using an eLBP for the prevention of antibiotic-induced dysbiosis and its associated pathologies. He received his B.S. and M. Sc. in Microbiology from Universidad de los Andes in Bogotá, Colombia. Andrés obtained his Ph. D. in Microbiology from the Massachusetts Institute of Technology under the mentorship of Institute Professor Sallie W. Chisholm. For his postdoctoral work, Andres joined the laboratory of Dr. James J. Collins at MIT where he applied synthetic biology approaches to endow bacteria with diagnostic and therapeutic capabilities.

Thesis : Ecology and evolution of lanthipeptides in marine picocyanobacteria

Thesis : Allosteric activation ofperiplasmic HtrA proteases

Thesis : Impacts of mucins on microbialphysiology and interactions

Thesis : Niche adaptations of the vibrionaceae,from the coastal ocean to the laboratory

Thesis : Prochlorococcus: life in light

Thesis : Exploiting fitness trade-offs to prevent antifungal drug resistance

Thesis : Identification and characterization of Toxoplasma gondii effectors that modulate innate immune pathways

Thesis : Aneuploidy causes proteotoxic stress in Saccharomyces cerevisiae

Mark Smith is a Co-Founder and the Chief Executive Officer of Finch Therapeutics. Mark is a recognized leader in the microbiome field, with over 50 peer-reviewed publications focused on the microbiome. Previously, Mark served as President and Research Director of OpenBiome, a nonprofit organization he co-founded for the purpose of expanding safe access to microbiota transplantation and catalyzing research into the human microbiome. He currently serves on the board of directors of Freya Biosciences, a privately-held biotechnology company.

Mark has a BA in biology from Princeton University and a PhD in microbiology from the Massachusetts Institute of Technology.

• Thesis : Ecological insights from bacterial networks
• 2017 Forbes 30 Under 30 List for Science

Thesis : Characterization of a bifunctional cell wall hydrolase in the mobile genetic element ICEBsJ

Thesis : Consequences of a mobile genetic element integrated at secondary locations