Publications
The EXFAB Biofoundry: Accelerating Biotechnology From Extreme and Exceptional Microorganisms
Ian Wheeldon
2026
Existing biofoundries typically handle microorganisms that are easy to grow, domesticate, and proliferate under laboratory conditions. To realize the promise of synthetic biology, there is a critical need for user platforms that are dedicated to a new generation of synthetic biology - one that focuses on discovering, phenotyping, and engineering new environmental isolates, microbial communities, and microbes with extreme phenotypes. With this motivation, a collaborative team from UC-Riverside (UCR), UC-Santa Barbara (UCSB), and CalPoly-Pomona (CPP) have established the BioFoundry for Extreme & Exceptional Fungi, Archaea and Bacteria (… Read more
Accelerating synthetic biology tools for anaerobes and anaerobic microbial communities
Michelle O'Malley
2026
Accelerating synthetic biology tools for anaerobes and anaerobic microbial communities at ACS Spring 2026, Atlanta Georgia, Georgia World Conference Center
Phenotypic: A modular python image analysis framework for microbial phenotyping
Eva Ottum
2026
Phenotypic: A modular python image analysis framework for microbial phenotyping at ACS Spring 2026, Atlanta Georgia, Georgia World Conference Center
Phenotyping of Rhodotorula spp. for heavy metal bioremediation applications
Christian Ona
2026
Phenotyping of Rhodotorula spp. for heavy metal bioremediation applications at ACS Spring 2026, Atlanta Georgia, Georgia World Conference Center
Developing an anaerobic cell-free protein expression platform for high throughput screening
Janelle Arnold
2026
Developing an anaerobic cell-free protein expression platform for high throughput screening at ACS Spring 2026, Atlanta Georgia, Georgia World Conference Center
Microfluidic platforms for high-throughput isolation and study of anaerobic and extremophilic microbes
Gaurav Argarwal
2026
Microfluidic platforms for high-throughput isolation and study of anaerobic and extremophilic microbes at ACS Spring 2026, Atlanta Georgia, Georgia World Conference Center
Panel: “BioFoundry Meets Users: How Biofoundries Rewrite the Paradigms of Discovery and Innovation"
Michelle O'Malley
2026
Panel: “BioFoundry Meets Users: How Biofoundries Rewrite the Paradigms of Discovery and Innovation” at the ACS Spring 2026, Atlanta Georgia, Georgia World Conference Center
Data to design: ExFAB’s Integrated workflows for AI/ML-driven functional genomics
Ian Wheeldon
2026
Data to design: ExFAB’s Integrated workflows for AI/ML-driven functional genomics at ACS Spring 2026, Atlanta Georgia, Georgia World Conference Center
ExFAB, the NSF-funded BioFoundry for Extreme and Exceptional Microbes, is building the experimental–computational pipeline required for AI- and ML-enabled biology — from automated data generation to predictive model development. A central focus is… Read more
Genomic and phenotypic comparison of Terrestrial and Aquatic Rhodotorula yeasts
Jason Stajich
2026
Genomic and phenotypic comparison of Terrestrial and Aquatic Rhodotorula yeasts at Fungal Genetics Conference, Pacific Grove, CA, Asilomar Conference Grounds
Abstract:
Aquatic and marine environments can harbor specialist and generalist fungi exhibiting filamentous and yeast morphologies. Rhodotorula yeasts are red and orange pigmented basidiomycetes found in a broad range of… Read more
Development of genetic transformation methods in anaerobic gut fungi
Hugh Purdy
2026
Development of genetic transformation methods in anaerobic gut fungi at Fungal Genetics Conference, Pacific Grove, CA, Asilomar Conference Grounds
Abstract:
Microorganisms hold great promise for applications in biotechnology, including the renewable production of fuels and chemicals, the biosynthesis of therapeutics, and even the creation of novel materials. However, it is well known… Read more
Automated discovery of stress-responsive natural products from anaerobic gut fungi in extreme environments
Rafael Solorzano
2026
Automated discovery of stress-responsive natural products from anaerobic gut fungi in extreme environments at Fungal Genetics Conference, Pacific Grove, CA, Asilomar Conference Grounds
Abstract:
Strict anaerobes from extreme environments harbor extensive but largely untapped biosynthetic potential. Yet natural products from these organisms remain poorly characterized because they are difficult to cultivate at scale and many of their biosynthetic pathways are not organized as contiguous gene clusters. In… Read more
Phenotyping of Rhodotorula tolerance to heavy metal contamination for bioremediation applications
Christian Ona
2026
Phenotyping of Rhodotorula tolerance to heavy metal contamination for bioremediation applications at Fungal Genetics Conference, Pacific Grove, CA, Asilomar Conference Grounds
Abstract:
Rhodotorula is an extremotolerant generalist yeast that has been isolated from a wide range of locations, from food spoilage, soils, plants, dishwashers, to more extreme conditions such as the International Space Station… Read more
Implementation of robotics and high-throughput imaging to capture growth rate data for Neurospora crassa cultured under different conditions
Monique Quinn
2026
Implementation of robotics and high-throughput imaging to capture growth rate data for Neurospora crassa cultured under different conditions at Fungal Genetics Conference, Pacific Grove, CA, Asilomar Conference Grounds
Abstract:
Growth rate is an important metric for determining the virulence of plant pathogens, the suitability of an organism for biotechnological applications, species… Read more
Identification of Functional Promoters in Anaerobic Gut Fungi
Elaine Kirschke
2026
Lignocellulose is the most abundant renewable carbon source on Earth, yet its recalcitrance remains a major bottleneck in biofuel and bioproduct production. Anaerobic gut fungi (AGF; phylum Neocallimastigomycota) initiate lignocellulose deconstruction in herbivore gut microbiomes under anaerobic conditions. Although they represent a minority of the community, AGF encode expansive repertoires of carbohydrate-active enzymes with broad substrate specificity, making them promising platforms for lignocellulose bioprocessing. However, functional characterization and engineering of AGF remain limited by genetic intractability. Highly AT-rich and… Read more
The ExFAB Biofoundry: Accelerating Biotechnology from Extreme & Exceptional Microorganisms
Michelle O'Malley
2026
The ExFAB Biofoundry: Accelerating Biotechnology from Extreme & Exceptional Microorganisms at JGI-EMLS User Meeting: Integrating Experimentation with Data
Native metabolomics identifies pteridines as CutA ligands and modulators of copper binding
Karoline Steuer-Lodd, Daniel Petras, Nouneh Boodaghian, Berenike C. Wagner , Christian Geibel , Amelie Stadelmann, Johanna Rapp, Hannes Link, Tilman Schramm, Ansel Hsiao, Eva Nussbaum, Heinz-Paul Grenzendorfer, Reinhard Albrecht, Marcus D. Hartmann, Karl Forchhammer, Khaled A. Selim , Chambers C. Hughes
2025
CutA, a conserved protein across all domains of life, has been suggested to be involved in copper tolerance in bacteria, though recent studies have questioned this association, leaving its biological role unknown. To clarify its function, we studied cutA knockout mutants from two phylogenetically distant species, Synechococcus elongatus PCC 7942 and Escherichia coli, using phenotyping combined with metabolomics. To investigate the interaction of CutA with potential substrates and cofactors, we performed a series of native metabolomics experiments with CutA and cell extracts from which… Read more
Developing an Anaerobic Cell-Free Protein Expression Platform for Discovery of Novel Enzyme Function
Carolyn Mills
2025
From the human gut to the soils that support plant growth, many of the microbes that support life thrive in anaerobic environments. These microbes often thrive in these environments by producing proteins that facilitate unique chemical transformations; notable examples include lignocellulosic biomass degradation and nitrogen fixation. To date, however, our ability to harness and engineer these functionalities has been stymied by challenges associated with mapping gene to function relationships in anaerobic organisms. These include a lack of genetic tools for non-model, anaerobic organisms and difficulties with heterologous expression… Read more
Nature vs Nurture: Interrogating the intrinsic and extrinsic drivers of emergent protein behaviors using data-driven approaches
Natasha Jones
2025
Nature vs Nurture: Interrogating the intrinsic and extrinsic drivers of emergent protein behaviors using data-driven approaches at AI-Driven Approaches to Emergent Protein Behaviors, Stowers Institute for Medical Research, Kansas City, MO
Automated QIAseq FX DNA Library Preparation on the Opentrons FLEX
Alexander Carrillo , Leonardo Sanchez Zamora, Zenan Xing, Jason Stajich, Ian Wheeldon
2025
DOI #10.17504 This workflow automates DNA-library construction for next generation Illumina short read sequencing by integrating the QIAseq FX DNA Library Kit with the Opentrons FLEX liquid-handling platform. A single FLEX script performs fragmentation, end-repair/A-tailing, adapter ligation, and bead clean-ups, eliminating manual pipetting and standardizing large-scale library preparation in 96-well plate format. The protocol yields consistent, high-quality libraries ready for short read sequencing while… Read more
Understanding and characterization of unusual metabolic pathways in anaerobic microbes
Bo Zhang
2025
Understanding and characterization of unusual metabolic pathways in anaerobic microbes at Center for Polymers and Organic Solids; seminar at UCSB.
Building the Biofoundry for Extreme and Exceptional Fungi, Archaea, and Bacteria, ExFAB
Ian Wheeldon
2025
Building the Biofoundry for Extreme and Exceptional Fungi, Archaea, and Bacteria, ExFAB at Summit of Synthetic Biology Centers, Rice Global Paris Center and Club de la Chasse
ExFAB (Panel - NSF BioFoundries Program)
Ian Wheeldon
2025
ExFAB - Panel of NSF BioFoundries Program at the Global BioFoundry Alliance Annual Meeting, University of Illinois Urbana Champaign, Carl R. Woese Institute for Genomic Biology, Conference Room 612
Kingdom-wide CRISPR guide design with ALLEGRO
Amirsadra Mohseni, Reyhane Ghorbani Nia, Aida Tafrishi, Mario León López, Xin-Zhan Liu, Jason Stajich, Stefano Lonardi, Ian Wheeldon
2025
DOI #: 10.1093 Designing CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) single guide RNA (sgRNA) libraries targeting entire kingdoms of life will significantly advance genetic research in diverse and underexplored taxa. Current sgRNA design tools are often species-specific and fail to scale to large, phylogenetically diverse datasets, limiting their applicability to comparative genomics, evolutionary studies, and biotechnology. Here, we introduce ALLEGRO, a combinatorial optimization algorithm designed to compose minimal, yet highly effective… Read more
The initial results and procedures of phenotyping UV-C tolerance
Christian Ona
2025
The initial results and procedures of phenotyping UV-C tolerance at Mycological Society of America (MSA) 2025 conference in Madison, Wisconsin
Building a Biofoundry to Accelerate Biotechnology from Extreme & Exceptional Microorganisms
Michelle O'Malley
2025
A collective of research projects aimed at “domesticating” environmental microbes, with a focus on engineering anaerobes that work together in complex communities to decompose and recycle carbon biomass throughout the Earth – from our guts to landfills and compost piles. Despite their importance, little information exists to parse the role of each microbial member within their dynamic community. To address these knowledge gaps, we pioneered new techniques to isolate anaerobes from biomass-rich environments (e.g. guts and fecal materials of herbivores), characterize their shared metabolism, and engineer synthetic microbiomes to drive… Read more
Developing a Cell-free Protein Synthesis Platform for Anaerobic Gut Fungi
Janelle Arnold, Michelle O'Malley, Carolyn Mills
2025
Advancements in cell-free protein synthesis (CFPS) have enabled the rapid prototyping of genetic circuits and biosynthetic pathways in E. coli, bypassing traditional time-intensive cloning workflows. This same technology stands to benefit non-model microbes that lack the genetic toolkits necessary for creating genetically modified mutants in implementing design-build-test-learn cycles. Our group is interested in the metabolic activity of anaerobic gut fungi (AGF) isolated from the guts of ruminant herbivores. AGF grow natively on lignin-rich substrates and could be used for microbial bioprocessing of lignocellulosic biomass… Read more
Understanding and engineering hydrogen production in anaerobic gut fungi
Bo Zhang, Scott Baker, Michelle O'Malley, Jan Tachezy, Ivan Hrdy
2025
Anaerobic gut fungi (AGF) decompose lignocellulosic substrates into fermentable sugars through the production of powerful enzymes, and they are attractive targets for waste to fuel applications. A recently constructed genome-scale metabolic model of AGF provides a framework to guide strain engineering efforts, especially to control the fungal fermentation byproducts formate, acetate, ethanol, lactate, succinate, and H2. However, the model’s accuracy is compromised because the core metabolic pathways in the fungal hydrogenosome (a hydrogen producing organelle) are unknown. In particular, the enzyme(s) that regenerate oxidized… Read more
Increased aridity is associated with diversity and composition changes in the biocrust mycobiome
Kian Kelly, Xinzhan Liu, Jared Croyle, Jason Stajich
2025
DOI #: 10.1101 Drylands comprise 45% of Earth’s land area and contain ecologically critical soil surface communities known as biocrusts. Biocrusts are composed extremotolerant organisms including cyanobacteria, microfungi, algae, lichen, and bryophytes. Fungi in biocrusts help aggregate these communities and may form symbiotic relationships with nearby plants. Climate change threatens biocrusts, particularly moss biocrusts, but its effects on the biocrust mycobiome remain unknown. Here, we performed a culture-dependent and metabarcoding survey of the moss biocrust… Read more
Pangenomes of Rhodotorula from Extreme Environments and of the Amphibian Pathogen Batrachochytrium
Jason Stajich
2025
The current projects are exploring the genomic and phenotypic diversity of Rhodotorula fungi collected from a range of extreme environments, evolution of the pan-genome of Aspergillus fumigatus, and DNA mycovirus discovery in chytrid fungi.
An argument for using anaerobes as microbial cell factories to advance synthetic biology and biomanufacturing
Thomas S. Lankiewicz, Nathalie H. Elisabeth, David L. Valentine, Michelle A. O'Malley
2025
DOI #: 10.1002 Anaerobes thrive in the absence of oxygen and are an untapped reservoir of biotechnological potential. Therefore, bioprospecting efforts focused on anaerobic microbial diversity could rapidly uncover new enzymes, pathways, and chassis organisms to drive biotechnology innovation. Despite their potential utility, anaerobic fermenters are viewed as inefficient from a biochemical perspective because their metabolisms produce fewer ATP (~2) per molecule of glucose processed than heterotrophic respirers (~32–38 ATP). While aerobes excel at ATP generation, they are… Read more