Benjamin Woolston
Assistant Professor,
Chemical Engineering
Affiliated Faculty,
Bioengineering
Office
- 223 Cullinane
- 617.373.5560
Lab
- 006 Mugar
Research Focus
Metabolic engineering and synthetic biology for sustainable biochemical production and human health
About
Joined the Chemical Engineering department in January 2020.
Education
- PhD in Chemical Engineering, Massachusetts Institute of Technology, 2017
- BSc in Chemical Engineering, The Pennsylvania State University, 2011
Honors & Awards
- 2025 NSF CAREER Award
- 2025 ONR Young Investigator Award
- 2025 Fostering Engineering Innovation in Education Award
- 2024 Søren Buus Outstanding Research Award
- 2020 International Metabolic Engineering Society Jay Bailey Young Investigator Award in Metabolic Engineering
- 2021 Biotechnology & Bioengineering Daniel IC. Wang Young Investigator Award
- 2021 MassVentures ACORN Innovation Award. Role: PI
- 2021 ARPA-E ECOSynBio – “Zero-Carbon Biofuels: An Optimized Two-Stage System for High Productivity Conversion of CO2 to Liquid Fuels.” Role: Co-PI
- 2022 SPARK Fund. Role: PI
- 2022 NIH NIBIB R21 Trailblazer – “Engineered Probiotics for Closed-Loop Control of Disease-Associated Gut Metabolites in Gut-on-Chip Models.” Role: PI
Teaching Interests
- Biochemical Engineering (CHME 5630)
- Graduate Kinetics and Reactor Design (CHME 7340)
Professional Affiliations
- American Institute of Chemical Engineers
- American Chemical Society
- American Association for the Advancement of Science
Research Overview
Metabolic engineering and synthetic biology for sustainable biochemical production and human health
Renewable Biochemical Production with Acetogenic Microbes
Biological production of chemicals and fuels can offer many environmental benefits, from pollution prevention to greenhouse gas capture and sequestration. Acetogenic microbes are a diverse group of ancient anaerobic bacteria that metabolize single carbon substrates such as carbon monoxide, methanol, and formic acid. These substrates have recently emerged as attractive feedstocks for bioprocessing because they do not compete with food supply, and can be produced directly from carbon dioxide using renewable energy. Using tools from metabolic engineering, synthetic biology, and protein biochemistry, we are investigating fundamental questions about the metabolism of acetogens, as well as engineering them to produce valuable biofuels and biochemicals using single carbon substrates.
Interrogating Microbial Metabolism in Human Gut Microbiota with Engineered Microbes
In recent years, the gut microbiota has emerged as an important factor in human health, and interactions between host and microbial cells mediated by small-molecule microbial metabolites play a role in regulating the immune system, gastrointestinal diseases and certain cancers, and a communication network between the brain and gut (gut-brain-axis) that affects neurodegeneration and mood. Studying the role of these metabolites in disease is complicated by the lack of robust methods to determine and modulate their local concentration in the gut. We are tackling this problem using synthetic biology methods to engineer commensal bacteria to sense and precisely modulate specific metabolites in vivo. Applications of these engineered microbes may give insight into disease pathways, impact of specific metabolites on the gut ecosystem, and a better mechanistic understanding of bacteria-host interactions.
Selected Research Projects
- Metabolic ‘Doping’ To Enhance Production of Biochemicals From Sustainable C1 Feedstocks
- – Principal Investigator, National Science Foundation
- Expanding the Product Range of Anaerobic Methanol Fermentation
- – Principal Investigator, Office of Naval Research
- New Approaches to Rapidly Domesticate Non-model Clostridia for Applications in Sustainability and Human Health
- – Principal Investigator, National Science Foundation
- Synthetic Ecology of Mixed Aerobic/Anaerobic Microbial Consortia
- – Principal Investigator, National Science Foundation
- Engineered Probiotics for Closed-Loop Control of Disease-Associated Gut Metabolites in Gut-On-Chip Models
- – Principal Investigator, National Institute of Biomedical Imaging and Bioengineering
Department Research Areas
Selected Publications
At Northeastern:
- Development of a recombineering system for the acetogen Eubacterium limosum with Cas9 counterselection for markerless genome engineering2024. ACS Synthetic Biology. AcceptedPA Sanford, BM WoolstonPreprint on bioRxiv
- An efficient Cre-based workflow for genomic integration and expression of large biosynthetic pathways in Eubacterium limosum2024. Biotechnology and Bioengineering, 1–7PA Sanford, I Blaby, Y Yoshikuni, BM WoolstonFull textPreprint
- Engineered bacteria titrate hydrogen sulfide and induce concentration-dependent effects on the host2023. Cell Reports 42 (12)JA Hayes, AW Lunger, AS Sharma, MT Fernez, RL Carrier, AN Koppes , R Koppes, BM WoolstonFull TextPreprint on bioRxiv
- Bacterial amylases enable glycogen degradation by the vaginal microbiome2023. Nature Microbiology 8 (9) 1641-1652DJ Jenkins*, BM Woolston*, MI Hood-Pishchany, P Pelayo, AN Konopaski, MQ Peters, MT France, J Ravel, CM Mitchell, S Rakoff-Nahoum, C Whidbey, EP BalskusFull Text* denotes equal authorship
- Native Gastrointestinal Mucus: Models and Techniques for Studying Interactions with Drugs, Drug Carriers, and Bacteria2023. Advanced Drug Delivery Reviews 114966CM Wang, MT Fernez, BM Woolston, RL CarrierFull Text
- Deletion of biofilm synthesis in Eubacterium limosum ATCC 8486 improves handling and transformation efficiency2023. FEMS Microbiology Letters 370PA Sanford, KG Miller, KO Hoyt, BM WoolstonFull Text
- Engineering bacteria for production of sustainable polycyclopropanated jet fuel alternatives2022. Trends in Biotechnology 40 (12) 1399-1400BM WoolstonFull Text
- Expanding the genetic engineering toolbox for the metabolically flexible acetogen Eubacterium limosum2022. Journal of Industrial Microbiology and Biotechnology 49 (5)PA Sanford, BM WoolstonFull Text
- Adapting isotopic tracer and metabolic flux analysis approaches to study C1 metabolism2022. Current Opinion in Biotechnology 75, 1052695KO Hoyt, BM WoolstonFull Text
- Synthetic or Natural? Metabolic engineering for assimilation and valorization of methanol2022. Current Opinion in Biotechnology 74, 171-179PA Sanford, BM WoolstonFull Text
- Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation2022. Nature Microbiology 7 (3) 434-450SM Bloom, NA Mafunda, BM Woolston, MR Hayward, JF Frempong, AB Abai, J Xu, AJ Mitchell, X Westergaard, FA Hussain, N Xulu, M Dong, KL Dong, T Gumbi, FX Ceasar, JK Rice, N Choksi, N Ismail, T Ndung’u, MS Ghebremichael, DA Relman, EP Balskus, CM Mitchell, DS KwonFull Text
Prior to Northeastern
- BM Woolston, G Stephanopoulos (2020). Engineering E. coli to Grow on Methanol. Joule, 4 (10),2070-2072.
- DF. Emerson, BM Woolston, N. Liu, M. Donnelly, D.H. Currie, G. Stephanopoulos, Enhancing Hydrogen‐Dependent Growth of and Carbon Dioxide Fixation by Clostridium Ljungdahlii Through Nitrate Supplementation, Biotechnology and Bioengineering, 116(2), 2019, 294-306
- T.B. Roth, BM Woolston, G. Stephanopoulos, D.R. Liu, Phage-Assisted Evolution of Bacillus methanolicus Methanol Dehydrogenase 2, ACS Synthetic Biology, 8(4), 2019, 796-806
- BM Woolston, T. Roth, I. Kohale, D.R. Liu, G. Stephanopoulos, Development of a Formaldehyde Biosensor with Application to Synthetic Methylotrophy, Biotechnology and Bioengineering, 2018
- BM Woolston, J.R. King, M. Reiter, B. Van Hove, G. Stephanopoulos, Improving Formaldehyde Consumption Drives Methanol Assimilation in Engineered E. Coli, Nature Communications, 9(1), 2018, 2387
- BM Woolston, D.F. Emerson, D.H. Currie, G. Stephanopoulos, Rediverting Carbon Flux in Clostridium Ljungdahlii Using CRISPR Interference (CRISPRi), Metabolic Engineering, 48, 2018, 243-253
Jun 10, 2025
PhD Spotlight: Justin Hayes, PhD’25, Chemical Engineering
Justin Hayes, PhD’25, chemical engineering, focuses on understanding how gut microbial metabolism impacts human health. He is an inventor on the pending patent and founder and CEO of Concordance Therapeutics Inc. He was awarded the Northeastern University chapter of the National Academy of Inventors Student Innovation Impact Award.
Jun 02, 2025
NSF CAREER Award To Advance Sustainable Biochemical Production
ChE Assistant Professor Benjamin Woolston received a $575,765 NSF CAREER award for “Metabolic ‘Doping’ To Enhance Production of Biochemicals From Sustainable C1 Feedstocks.” The research aims to understand the regulation of carbon metabolism and use the insight to make acetogens more effective for renewable production of fuels and chemicals.
Feb 03, 2025
ONR Young Investigator Award for Engineering Clostridia Microbes
ChE Assistant Professor Benjamin Woolston received a Young Investigator Award from the Office of Naval Research for “Expanding the Product Range of Anaerobic Methanol Fermentation.” He is engineering Clostridia microbes that absorb methanol and convert them into a protein-based biomass deriving a wide range of materials, from food to plastics.
Jan 30, 2025
Faculty and Staff Awards 2025
Faculty and staff were recognized at the 27th Annual College of Engineering Faculty and Staff Awards for their exceptional service and dedication in support of students, the COE community, and the university during the 2024-2025 academic year.
Sep 27, 2024
A Microbial Solution for a Sustainable Future
ChE Assistant Professor Ben Woolston is using engineered microbes to convert carbon dioxide into valuable products like fuels and chemicals, offering a sustainable alternative to traditional petrochemical and corn-based production methods.
Aug 27, 2024
$1.27M NSF Award for Engineering Clostridia for Sustainability and Human Health
ChE Assistant Professor Benjamin Woolston, in collaboration with Tulane University and Tufts University, was awarded a $1.27 million NSF grant for “New Approaches to Rapidly Domesticate Non-model Clostridia for Applications in Sustainability and Human Health.” The research team will develop novel approaches to streamline genetic engineering of Clostridia.
Jul 03, 2024
Improving the Smell of Composting
A team of bioengineering students are participating in the International Genetically Engineered Machine Foundation global competition that showcases synthetic biology projects. The iGEM student team is developing a solution that would make compost smell like mint and lavender by targeting the microbial process. They also recently received a PEAK Experience Award from Northeastern.
Jul 02, 2024
Studying Gut Bacteria
ChE Assistant Professor Benjamin Woolston, in collaboration with Ahmad (Mo) Khalil from Boston University, was awarded a $900,000 NSF grant for “Synthetic Ecology of Mixed Aerobic/Anaerobic Microbial Consortia.”
May 07, 2024
Summer 2024 PEAK Experiences Awardees for Undergrad Research
Several engineering and science students mentored by COE faculty are recipients of the Summer 2024 PEAK Experiences Awards from Northeastern’s Office of Undergraduate Research and Fellowships.
Feb 01, 2024
Faculty and Staff Awards 2024
The College of Engineering recognized faculty and staff at the annual faculty and staff awards event and thanked everyone for their hard work and dedication in support of our students, college, and university during the 2023-2024 academic year. View award recipients and photo gallery.