Topic Area

Biocatalysis and Protein Engineering

The Biocatalysis sessions of SIMB cover the fundamental and applied science of enzyme characterization, design, improvement, various feedstock conversion, and view the microbe as a catalyst for industrial applications. Topics cover protein structural biology, computational modeling, biochemical lignocellulosic conversion, conversion or upgrading of waste streams, P450s, enzymes from extremophiles, and microbial conversion in native and engineered pathways. Biocatalysis is a sustainable and environmentally-friendly practice and its industrial application can reduce the cost compared to strictly thermochemical processes as the result of higher selectivity and diverse condition optima, while reducing the reaction time, production costs and industrial waste. This topic area will focus on current success and future outlooks for biocatalysis applications in the production of various goods ranging from conventional metabolites, proteins, food, drugs, fuels and industrial chemicals.

Topic Chairs

Ross Thyer – Rice University
Bjorn Traag – Aralez Bio
Josh Michener – Oak Ridge National Laboratory

Sessions

Efficient utilization of alternative feedstocks for production of biofuels and bioproducts can enhance biorefinery economics and provide significant environmental benefits, including waste management and greenhouse gas reductions. However, the challenges unique to these feedstocks (e.g., lignin, plastics, and other waste streams) can include energy or chemically intensive pretreatment, potentially toxic pretreatment byproducts, slow feedstock degradation, and often varied mixtures of carbon monomers to utilize. This session highlights recent advances in the development of industrially relevant enzymatic and microbial biocatalysts that harness alternative feedstocks for transformation into value-added fuels or chemicals.

Conveners

Trevor Nicks – Caravel
Will Cordell – National Laboratory of the Rockies (NLR)

Recent years have seen an explosive advance in techniques for augmenting and accelerating classical directed evolution approaches for enzyme evolution. This session will highlight the state-of-the-art strategies in computational design, machine learning and screening methodologies to accelerate enzyme engineering.

Conveners

Karla Camacho Soto – Merck
Soumitra Athavale – UCLA

Industrial biocatalysis enables flexible, selective, and sustainable synthesis of fuels, chemicals, materials, therapeutics, and food ingredients from renewable feedstocks. Commercial deployment at scale requires integrated understanding of catalyst performance, process economics, and operational challenges such as stability, reactor performance, contamination control, and separations. This session will feature real-world examples of biocatalytic scale-up and discuss strategies to overcome scale-related barriers. Emphasis will be placed on emerging approaches, including AI-assisted enzyme/strain design, advanced process analytics, and integrated bioprocess platforms, that enhance robustness and commercial viability of industrial bioproduction.

Conveners

Dongming Xie – UMass Lowell
David Walker – ERDC

The “Frontiers of Chemistry and Biocatalysis” session will focus on the development of new biocatalysts that advance innovative directions in catalysis. A broad range of topics will be featured in this session, including expanding enzyme substrate specificity to non-native or non-natural products and new biomolecular or computational methods to facilitate such engineering. Also of interest are efforts to identify new metabolic pathways, or any other examples that push the boundaries of chemistry at the enzyme or whole pathway level.

Conveners

Yannick Bomble – National Laboratory of the Rockies (NLR)
Amy Fraley – ETH Zurich

Topic Area

Fermentation and Biomanufacturing

Unconventional biomanufacturing encompasses a broad range of innovative and non-traditional methods to produce biological products. This includes the utilization of non-traditional raw materials and may involve the integration of cutting-edge technologies, such as synthetic biology, metabolic engineering, and novel fermentation processes. Biomanufacturing involves the use of not just living cells such as bacteria, yeast, or mammalian cells, but could use cell-free systems to produce various products like pharmaceuticals, enzymes, biofuels etc and renewable electrons to facilitate carbon-negative products. Cell-free systems utilize cellular extracts for the production of target molecules, small and large, and offer several advantages, including speed and ease of optimization. It is also a flexible platform that enables the production of small molecules, proteins, enzymes, vaccines, to name a few. This session will focus on the development and biomanufacturing of products using a variety of unconventional techniques and feedstocks.

Topic Chairs

Neal Connors – Phoenix BioConsulting, LLC
Sarita Chauhan – GEA
Chris Stowers – Kerry

Sessions

Microbes have evolved to utilize a diverse array of carbon molecules for growth as single microorganisms or in microbial communities. This session will highlight microbial conversion of C1 and C2 compounds, such as CO, CO2, acetate, methanol, methane, formate and acetate into high value fuels and chemicals. Topics will span methylotrophic and autotrophic chassis development, pathway engineering and novel integration strategies to maximize carbon conversion. Presenters will contextualize their research integrating fundamental science and industrial applications with an understanding of the technoeconomic and life-cycle impacts of a scaled process.

Conveners

Michael Resch – National Laboratory of the Rockies
Alfred Spormann – Stanford University/CORC

Microorganisms are increasingly recognized as key platforms for food production. Their rapid growth, high nutritional value, ability to utilize diverse non-traditional feedstocks combined with the advancements in synthetic biology and precision fermentation offer advantages that are uniquely complementary to conventional agricultural systems. However, major challenges must be overcome in translating laboratory-scale strain development into robust, scalable, and economically viable production processes. This session focuses on bridging microbial strain design and industrial implementation. The topics include advanced breeding, synthetic biology, and metabolic engineering strategies for robust fermentation, end-to-end bioprocess design for large-scale production, and the use of technoeconomic and life cycle analyses to assess feasibility and sustainability. In addition, the integration of artificial intelligence and data-driven approaches for optimizing microbial food production will be discussed. Together, these perspectives highlight pathways for advancing microbial food technology from proof-of-concept to industrial reality.

Conveners

Sarita Chauhan – GEA Systems
Hiroshi Takagi – Nara Institute of Science and Technology
Timothy Barnett – GEA Systems

Biomanufacturing is enabling the development of innovative technologies and processes that are critical to industrial and defense supply chains. This session will showcase examples of practical advancements in fermentation and biomanufacturing that are driving scalable, efficient, and sustainable bioprocesses for applications beyond traditional sectors such as healthcare and food. Invited speakers will highlight how these technologies are being applied to produce high-performance materials, support resource security, and enhance infrastructure capabilities. By focusing on real-world applications, this session will demonstrate the potential of biomanufacturing to address supply chain challenges and meet critical needs across diverse industries.

Conveners

Annie Crumbley – U.S. Army DEVCOM CBC
Nancy Kelley-Loughnane – AFRL

This session will explore lessons learned from bioprocess scale-up failures and recoveries, emphasizing how early decisions—such as strain selection, tank design, process control schemes, media decisions, and downstream strategies—can make or break industrial success. Speakers will share case studies of unexpected challenges encountered during scale-up and how they were addressed. The session will highlight the importance of anticipating scale-dependent variables like oxygen transfer, mixing, and nutrient gradients. Attendees will gain practical insights into designing robust, scalable processes from the outset to avoid costly surprises and ensure smoother transitions from lab to commercial production.

Conveners

Dale Brown – Corteva Agriscience
Katarina Midelfort – dsm-firmenich

Topic Area

Microbiomes and Environmental Microbiology

The Environmental sessions of SIMB Annual meeting covers a broad range involving the use of microbes for applications in environments outside of the laboratory or conventional biomanufacturing facilities. These sessions incorporate the development and application of microbes and microbial consortia for applications in human and environmental microbiomes as well as for the production or recovery of inorganic materials. This includes the use of genetic engineering to add new capabilities, modify existing phenotypes, or incorporate mechanisms to limit propagation of engineered microbes outside of target environments. Fundamental research and applied use of microbes to control the cycling of elements, such as nitrogen or phosphate, in agriculture and waste processing will be emphasized. Finally, sessions will also include applications or involvement of bacteria in the sustainable production, recovery, or environmental stability of inorganic materials such as concrete and valuable metals.

Topic Chairs

Kate Zhalnina – Lawrence Berkeley National Laboratory
Joshua Elmore – Pacific Northwest National Laboratory
Allison Werner – National Laboratory of the Rockies

Sessions

Engineered microbes are increasingly being designed to function beyond controlled bioproduction settings and within complex, real-world ecosystems. This session will highlight advances in the design, deployment, and performance of genetically modified microorganisms and communities operating “in the wild,” from mammalian gut ecosystems to agricultural fields and natural environments. Topics may include engineering strategies for plant growth promotion, bioremediation, and modulation of host-associated microbiomes, as well as emerging approaches for nutrient retention, ecological resilience, biocontainment, and limiting horizontal gene transfer. Together, these studies will examine both the opportunities and challenges of translating microbial engineering into biologically diverse, real-world systems.

Conveners

Nathan Crook – North Carolina State University
Jonathan Conway – Princeton University

Microorganisms offer powerful alternatives to energy-intensive and environmentally damaging thermochemical approaches for the recovery and valorization of critical minerals and valuable metals. This session will highlight microbial processes that enable metal mobilization, separation, concentration, and stabilization in natural and engineered systems. Topics may include advances in established approaches such as bioleaching and biomineralization, as well as emerging strategies for recovering critical minerals from low-grade ores, mine tailings, industrial wastes, and contaminated environments. The session will also explore new insights into the physiology and metabolic capabilities of metal-transforming microbes that underpin scalable, low-energy solutions for sustainable metal recovery and resource circularity.

Conveners

Joseph Cotruvo – The Pennsylvania State University
Pubudu Handakumbura – Pacific Northwest National Laboratory

Microorganisms play central roles in the cycling of critical macronutrients (e.g., nitrogen, phosphorus) and micronutrients (e.g., minerals) across complex environments. This session highlights advances in leveraging individual microbes, synthetic communities, and process-level engineering to control and optimize nutrient cycling and function in agricultural soils, controlled environment agriculture, waste-processing systems, and contaminated sites. Topics may include how interactions among engineered functions, microbial community composition, and environmental or process conditions contribute to beneficial outcomes such as increased crop productivity, enhanced carbon sequestration, reduced fertilizer inputs, and effective remediation of impacted environments.

Conveners

Joseph Edwards – Texas A&M University
Patricia Dorr de Quadros – GrowInCities Inc.

Microbial communities that thrive in extreme environments, such as high temperature, salinity, acidity, pressure, or metal-rich systems, harbor unique metabolic capabilities that enable novel materials and chemistries. These microbiomes are rich sources of novel biomolecules, enzymes, and metabolic pathways with applications in biotechnology, including pharmaceuticals, robust industrial enzymes, alternative food and protein sources, and advanced materials such as bioplastics and biosurfactants. This session will examine how extremophile metabolisms and community-driven processes unlock unconventional biological functions, mineral transformations, and materials synthesis, and how these traits can be engineered and deployed in scalable, sustainable biotechnological applications.

Conveners

Tanvi Govil – South Dakota School of Mines & Technology
Rajesh K Sani – South Dakota School of Mines & Technology

Topic Area

Metabolic Engineering

The Metabolic Engineering sessions of SIMB cover the fundamental approaches, tools, and applications associated with strain, pathway, and protein engineering for fuels and chemicals production. Talks in sessions are expected to cover topics in synthetic biology, engineering conventional/non-conventional microbes, microbial communities, predictive AI and ML computational approaches for engineering targets, and demonstrations of technologies and methods to realize production at increasing scales towards industrialization.

Topic Chairs

Jay Huenemann – Corteva Agriscience
Pamela Peralta-Yahya – Georgia Institute of Technology
Alissa Bleem – National Laboratory of the Rockies

Sessions

In recent years, access to automated laboratory systems has expanded, and new platforms have been developed that can manipulate samples, capture images, and monitor environmental conditions. The resulting increase in data generation can inform and advance the selection of metabolic engineering targets for strain improvement. The focus of this session will be the development of automated systems and their applications to accelerate metabolic engineering strategies.

Convener

Adam Feist – UCSD

Availability of new artificial intelligence tools and machine learning models has increased at an incredible rate in the last decade. Recent advances in AI/ML approaches have further augmented the abilities of computational approaches to leverage data and models to guide experimental design, thereby providing insights and recommendations about the biological spaces being explored. This session will focus on the developments in computational and systems approaches, including mechanistic modeling, empirical approaches, and applications of AI/ML strategies to metabolic engineering.

Convener

Stephen Lane – Cornell University

Advances in the detection, tracking, and modeling of metabolites have singificantly expanded our understanding of numerous microbial systems. This session will focus on advanced tools to model or predict metabolite flux and the application of these tools to drive metabolic engineering strategies.

Convener

Yinjie Tang – Washington University in St. Louis

Utilization of alternative feedstocks to produce biofuels and biochemicals can enhance biorefinery economics and provide significant environmental benefits including greenhouse gas reductions. Additionally, emerging biological and hybrid processes are expanding the role of biomanufacturing beyond fuels and chemicals to include strategic recovery of critical materials from unconventional resources. This session will showcase advances in microbial and metabolic engineering platforms designed to convert non-traditional feedstocks into drop-in fuels, high-value bioproducts, and recoverable critical materials.

Convener

Bradley Biggs – University of Michigan

Advanced genetic tools have been developed and utilized in model microbial systems to drive metabolic engineering for many years. Numerous non-model organisms have been identified in recent years which possess beneficial phenotypes such as unique carbon catabolism, redox and toxicity tolerances, and thermophilic growth capacity. The challenges of translating these phenotypes into model organisms remains a barrier, and thus developing genetic tools to engineer these non-model organisms is critical. This session will highlight advances in the development of genetic tools in non-model bacterial systems.

Convener

Austin Carroll – Oak Ridge National Laboratory

Advanced genetic tools have been developed and utilized in model microbial systems drive metabolic engineering for many years. Numerous non-model organisms have been identified in recent years which exhibit beneficial phenotypes such as unique carbon catabolism, redox and toxicity tolerance, and thermophilic tolerances. The challenges of translating these phenotypes into model organisms remains a barrier and thus developing genetic tools to engineering these non-model organisms is critical. This session will highlight advances in the development of genetic tools in non-model fungal systems.

Convener

Joanna Tannous – Oak Ridge National Laboratory

In recent years, there has been increased interest in utilizing the unique capabilities of microbes to address environmental issues through bioremediation or deconstruction of waste. Further, the application of microbes in agriculture to cycle nutrients, fix nitrogen, or deliver pest management compounds has also seen significant growth in use and interest. This session will focus on unique metabolic engineering strategies and tools which have advanced the use of microbes in the environment.

Convener

Eric Holmes – University of Idaho

Advances in experimental and computational tools have enabled metabolic engineering in a wide array of microbes for the synthesis of commercially relevant molecules. Moving from lab to manufacturing scale can negatively impact rates, titers, and yields of desired products. This session will focus on metabolic engineering strategies and processes used to overcome challenges in process scale-up.

Convener

Esha Khullar – Cargill
Audrey Diano – Independent Consultant

Topic Area

Natural Products

The Natural Products sessions of SIMB cover basic and applied science and technologies to discover, elucidate, and harness natural products or specialized metabolites from biological sources. Topics include biosynthetic pathway elucidation and reconstitution, enzymology, biochemistry, genomics, structure-activity relationships, mode of action, and ecology within natural product research. This program area specifically focuses on natural products from microbial, plant, and other eukaryotic sources in addition to engineering-biology applications of biosynthesis. Natural products continue to be an important and useful source of chemical diversity and novel bioactivities, and a plethora of recent technological innovations are accelerating the pace of discovery and application development.

Topic Chairs

Jaclyn Winter – University of Utah
Wenlong Cai – Brightseed
Barry O’ Keefe – National Institutes of Health

Sessions

Advances in genome mining, heterologous expression, and synthetic biology are redefining how natural products are discovered and produced. This session highlights innovative strategies, ranging from chassis engineering and pathway refactoring to automated high throughput strain construction, that unlock cryptic biosynthetic gene clusters, expand chemical diversity, and dramatically accelerate access to novel molecules.

Conveners

TBD

Natural products mediate key ecological interactions, ranging from microbial competition and symbiosis to modulation of host immunity and microbiome dynamics. This session explores advanced approaches to uncover molecular targets, elucidate mechanisms of action, map chemical communication networks, and integrate chemical biology with ecology and evolution.

Conveners

TBD

Nature continues to reveal extraordinary enzymatic transformations that challenge the limits of classical biochemistry. This session focuses on newly discovered catalysts, reaction mechanisms, and structure–function insights, as well as engineered biocatalysts that enable tailored modifications, late-stage diversification, and scalable biomanufacturing.

Conveners

TBD

Machine learning, artificial intelligence, and computational chemistry are transforming how we explore natural product chemical space. This session will feature innovations in predictive biosynthetic algorithms, metabolomic annotation tools, protein modeling, sequence-to-structure pipelines, and integrated computational platforms driving the next generation of natural product discovery.

Conveners

TBD

Topic Area

Special Sessions

Sessions

The rapid advancement of artificial intelligence is transforming industrial microbiology, offering powerful new tools that are reshaping the field from molecular discovery through to scaled manufacturing. This session brings together leading researchers and practitioners applying AI and machine learning across novel gene discovery, metabolic engineering, and protein and enzyme design, through fermentation optimization and bioprocess scale-up. Following the presentations, a moderated panel discussion will invite audience engagement on the key challenges and opportunities in harnessing AI across the full industrial biotechnology workflow — from laboratory discovery to commercial-scale production.

Conveners

Rob Donofrio – BioScope Innovations
Tim Davies – Corteva

Convener

Ramon Gonzales –

Scaling up innovative biomanufacturing technologies from bench to commercialization involves multifaceted technical and economic challenges. In this session experts will highlight through case studies, the production of biofuel, biochemicals, and alternative food and feeds, with focuses on Process Optimization and Production, Feedstock Choices, and Early-Stage Technoeconomic Analysis.

Conveners

Yan Zhang – National Corn-to-Ethanol Research Center
Andrew Manning – POET