About

Matthew Bennett is a Professor of BioSciences and the Director of the Systems, Synthetic, & Physical Biology Program at Rice University. His research spans the boundary between theoretical and experimental synthetic biology, with a particular focus on the dynamics of gene regulation. His work encompasses small-scale interactions such as transcription and translation, as well as the large-scale dynamics of gene networks and synthetic microbial consortia. Bennett employs an interdisciplinary approach to uncover the underlying design principles governing gene networks and microbial consortia, engineer novel synthetic gene circuits for practical applications, and develop new mathematical tools to better describe gene networks. The ultimate goal of his research is to develop synthetic multicellular systems for biomedical and environmental applications.

Research topics

• Computer Science
• Engineering
• Biology
• Genetics
• Computational biology
• Materials science
• Biochemical engineering
• Waste management
• Nanotechnology
• Cell biology

Selected publications

• Fast, long-range intercellular signal propagation through growth-assisted positive feedback

  Cell Systems · 2026-03-01

  articleSenior author
  PublisherDOI

• Engineering plasmids with synthetic origins of replication

  Nature Communications · 2026-02-02

  articleOpen access

  Plasmids remain by far the most common medium for delivering engineered DNA to microorganisms. However, the reliance on natural plasmid replication mechanisms limits their tunability, compatibility, and modularity. Here we refactored the natural pMB1 origin and created plasmids with customizable copy numbers by tuning refactored components. We then created compatible origins that use synthetic RNA regulators to implement independent copy control. We further demonstrated that the synthetic origin of replication (SynORI) can be engineered modularly to respond to various signals, allowing for multiplexed copy-based reporting of environmental signals. Lastly, a library of 6 compatible SynORI plasmids was created and co-maintained in E. coli for a week. This work establishes the feasibility of creating plasmids with SynORI that can serve as a biotechnology for synthetic biology. The reliance on natural plasmid replication mechanisms limits plasmid tunability, compatibility, and modularity. Here the authors refactor the natural pMB1 origin and create plasmids with customizable copy numbers with synthetic RNA regulators to implement independent copy control.

  PublisherOA PDFDOI

• Flow-induced 2D nanomaterials intercalated aligned bacterial cellulose

  Nature Communications · 2025-07-01 · 17 citations

  articleOpen access

  Bacterial cellulose is a promising biodegradable alternative to synthetic polymers due to the robust mechanical properties of its nano-fibrillar building blocks. However, its full potential of mechanical properties remains unrealized, primarily due to the challenge of aligning nanofibrils at the macroscale. Additionally, the limited diffusion of other nano-fillers within the three-dimensional nanofibrillar network impedes the development of multifunctional bacterial cellulose-based nanosheets. Here, we report a simple, single-step, and scalable bottom-up strategy to biosynthesize robust bacterial cellulose sheets with aligned nanofibrils and bacterial cellulose-based multifunctional hybrid nanosheets using shear forces from fluid flow in a rotational culture device. The resulting bacterial cellulose sheets display high tensile strength (up to ~ 436 MPa), flexibility, foldability, optical transparency, and long-term mechanical stability. By incorporating boron nitride nanosheets into the liquid nutrient media, we fabricate bacterial cellulose-boron nitride hybrid nanosheets with even better mechanical properties (tensile strength up to ~ 553 MPa) and thermal properties (three times faster rate of heat dissipation compared to control samples). This biofabrication approach yielding aligned, strong, and multifunctional bacterial cellulose sheets would pave the way towards applications in structural materials, thermal management, packaging, textiles, green electronics, and energy storage. NCOMMS-24-62603C. The potential applications of bacterial cellulose (BC) have been limited by challenges in aligning nanofibrils at the macroscale and creating BC-based multifunctional nanosheets. Here, the authors report a strategy of using shear forces from fluid flow in a rotational culture device to biosynthesize strong BC sheets with aligned nanofibrils, and BC-based multifunctional hybrid nanosheets.

  PublisherOA PDFDOI

• Long-term homeostasis in microbial consortia via auxotrophic cross-feeding

  Nature Communications · 2025-09-29 · 5 citations

  articleOpen accessSenior author

  Synthetic microbial consortia are collections of multiple strains or species of engineered organisms living in a shared ecosystem. Because they can separate metabolic tasks among different strains, synthetic microbial consortia have applications in developing biomaterials, biomanufacturing, and biotherapeutics. However, synthetic consortia often require burdensome control mechanisms to ensure that consortia members remain at the correct proportions. Here, we present a simple method for controlling consortia proportions using cross-feeding in continuous auxotrophic co-culture. We use mutually auxotrophic E. coli with different essential gene deletions and regulate the growth rates of members of the consortium via cross-feeding of the missing nutrients in each strain. We demonstrate precise regulation of the proportions by exogenous addition of the missing nutrients. We also model the co-culture’s behavior using a system of ordinary differential equations that enable us to predict its response to changes in nutrient concentrations. Our work provides a powerful tool for consortia proportion control with minimal metabolic costs to the constituent strains. Synthetic microbial consortia are collections of strains which can segregate metabolic tasks for efficient use in biomaterials, biomanufacturing, and biotherapeutics. Here, the authors present a method to maintain and tune the ratio of two co-cultured bacterial strains via growth medium manipulation.

  PublisherOA PDFDOI

• Engineering Plasmids with Synthetic Origins of Replication

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-21 · 4 citations

  preprintOpen access

  Plasmids remain by far the most common medium for delivering engineered DNA to microorganisms. However, the reliance on natural plasmid replication mechanisms limits their tunability, compatibility, and modularity. Here we refactor the natural pMB1 origin and create plasmids with customizable copy numbers by tuning refactored components. We then create compatible origins that use synthetic RNA regulators to implement independent copy control. We further demonstrate that the synthetic origin of replication (SynORI) can be engineered modularly to respond to various signals, allowing for multiplexed copy-based reporting of environmental signals. Lastly, a library of 6 orthogonal SynORI plasmids is created and co-maintained in E. coli for a week. This work establishes the feasibility of creating plasmids with SynORI that can serve as a new biotechnology for synthetic biology.

  PublisherDOI

• Long-term homeostasis in microbial consortia via auxotrophic cross-feeding

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-09

  preprintOpen accessSenior author

  Synthetic microbial consortia are collections of multiple strains or species of engineered organisms living in a shared ecosystem. Because they can separate metabolic tasks among different strains, synthetic microbial consortia have myriad applications in developing biomaterials, biomanufacturing, and biotherapeutics. However, synthetic consortia often require burdensome control mechanisms to ensure that the members of the community remain at the correct proportions. This is especially true in continuous culture systems in which slight differences in growth rates can lead to extinctions. Here, we present a simple method for controlling consortia proportions using cross-feeding in continuous auxotrophic co-culture. We use mutually auxotrophic E. coli with different essential gene deletions and regulate the growth rates of members of the consortium via cross-feeding of the missing nutrients in each strain. We demonstrate precise regulation of the co-culture steady-state ratio by exogenous addition of the missing nutrients. We also model the co-culture’s behavior using a system of ordinary differential equations that enable us to predict its response to changes in nutrient concentrations. Our work provides a powerful tool for consortia proportion control with minimal metabolic costs to the constituent strains.

  PublisherDOI

• Pattern Formation and Bistability in a Synthetic Intercellular Genetic Toggle

  ACS Synthetic Biology · 2024-08-30 · 3 citations

  articleSenior authorCorresponding

  Differentiation within multicellular organisms is a complex process that helps to establish spatial patterning and tissue formation within the body. Often, the differentiation of cells is governed by morphogens and intercellular signaling molecules that guide the fate of each cell, frequently using toggle-like regulatory components. Synthetic biologists have long sought to recapitulate patterned differentiation with engineered cellular communities, and various methods for differentiating bacteria have been invented. Here, we couple a synthetic corepressive toggle switch with intercellular signaling pathways to create a "quorum-sensing toggle". We show that this circuit not only exhibits population-wide bistability in a well-mixed liquid environment but also generates patterns of differentiation in colonies grown on agar containing an externally supplied morphogen. If coupled to other metabolic processes, circuits such as the one described here would allow for the engineering of spatially patterned, differentiated bacteria for use in biomaterials and bioelectronics.

  PublisherDOI

• Fast, long-range intercellular signal propagation through growth assisted positive feedback

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-12-05

  preprintOpen accessSenior authorCorresponding

  SUMMARY Intercellular signaling in bacteria is often mediated by small molecules secreted by cells. These small molecules disperse via diffusion which limits the speed and spatial extent of information transfer in spatially extended systems. Theory shows that a secondary signal and feedback circuits can speed up the flow of information and allow it to travel further. Here, we construct and test several synthetic circuits in Escherichia coli to determine to what extent a secondary signal and feedback can improve signal propagation in bacterial systems. We find that positive feedback-regulated secondary signals propagate further and faster than diffusion-limited signals. Additionally, the speed at which the signal propagates can accelerate in time, provided the density of the cells within the system increases. These findings provide the foundation for creating fast, long-range signal propagation circuits in spatially extended bacterial systems.

  PublisherOA PDFDOI

• Preserving Fresh Eggs via Egg‐Derived Bionanocomposite Coating

  Advanced Functional Materials · 2024-04-12 · 11 citations

  articleOpen access

  Abstract Egg waste is a major contributor to global food waste, accounting for 15% of discarded food in the United States. Typically, eggs have a shorter shelf life at room temperature and are preserved in refrigeration from production to consumption. However, maintaining constant refrigeration is energy‐intensive and expensive. Here, a bionanocomposite coating has been developed that incorporates each element of eggs – egg white, yolk, and eggshell – to increase the shelf life of fresh eggs without requiring further refrigeration. The quality of eggs has been successfully preserved for up to three weeks at room temperature. The coated eggs maintain the highest grade (AA) and exhibit improved Haugh Unit (HU), Yolk Index (YI), and pH compared to uncoated eggs. The coating reduces weight loss by ≈37% with an increase in HU (≈12.5%) and YI (≈13.9%). Morphological analysis reveals strong adhesion of the coating to the eggshell surface, showcasing promising barrier properties. The coating demonstrates an optimal combination of oxygen permeability (≈12.2 cm 3 µm m −2 d −1 kPa −1 ) and water vapor transmission (≈31.5 g mm m −2 per day) with excellent antimicrobial properties. Overall, this approach of repurposing eggs into a high‐performance coating shows a promising viable alternative to refrigeration and a solution to combat egg waste.

  PublisherOA PDFDOI

• Indirect enrichment of desirable, but less fit phenotypes, from a synthetic microbial community using microdroplet confinement

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-01-11 · 1 citations

  preprintOpen access

  Spatial structure within microbial communities can provide nearly limitless opportunities for social interactions and are an important driver for evolution. As metabolites are often molecular signals, metabolite diffusion within microbial communities can affect the composition and dynamics of the community in a manner that can be challenging to deconstruct. We used encapsulation of a synthetic microbial community within microdroplets to investigate the effects of spatial structure and metabolite diffusion on population dynamics and to examine the effects of cheating by one member of the community. The synthetic community was comprised of three strains: a ‘Producer’ that makes the diffusible quorum sensing molecule ( N -(3-Oxododecanoyl)-L-homoserine lactone, C12-oxo-HSL) or AHL; a ‘Receiver’ that is killed by AHL and a Non-Producer or ‘cheater’ that benefits from the extinction of the Receivers, but without the costs associated with the AHL synthesis. We demonstrate that despite rapid diffusion of AHL between microdroplets, the spatial structure imposed by the microdroplets allow a more efficient but transient enrichment of more rare and slower growing ‘Producer’ subpopulations. Eventually, the Non-Producer population drove the Producers to extinction. By including fluorescence-activated microdroplet sorting and providing sustained competition by the Receiver strain, we demonstrate a strategy for indirect enrichment of a rare and unlabeled Producer. The ability to screen and enrich metabolite Producers from a much larger population under conditions of rapid diffusion provides an important framework for the development of applications in synthetic ecology and biotechnology. Abstract Figure

  PublisherOA PDFDOI

Recent grants

• NIH Grant F32GM082168

  NIH · $90k · 2009

• Collaborative Research: MODULUS: A synthetic biology approach to understanding environment sensing in multicellular systems

  NSF · $359k · 2019–2022

• Experimental and mathematical analysis of delay in transcripitional signaling

  NIH · $1.4M · 2012–2018

• Collaborative Research: Spatiotemporal Dynamics of Synthetic Microbial Consortia

  NSF · $931k · 2017–2021

• Dynamics and pattern formation in differentiating cellular populations

  NIH · $1.2M · 2021–2026

Frequent coauthors

• Krešimir Josić́

  University of Houston

  53 shared

• William Ott

  University of Houston

  23 shared

• Jeff Hasty

  University of California, San Diego

  18 shared

• Razan N. Alnahhas

  Boston University

  13 shared

• David L. Shis

  Rice University

  12 shared

• Jae Kyoung Kim

  National Institute for Mathematical Sciences

  11 shared

• Andrew J. Hirning

  Rice University

  11 shared

• James J. Winkle

  University of Houston

  10 shared

Labs

• BennettlabPI

  Not provided

Education

• PhD, Physics

  Georgia Institute of Technology

  2006