Publications
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
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
Building a Sustainable Future with Lessons Learned from Unconventional Microbes
Michelle O'Malley
2025
Address ways in which biophysicists can engage with sustainability research, present concrete examples of research with strong impact on sustainability, discuss funding opportunities, and propose how to make your daily research practices more sustainable.
New approaches to secondary metabolite discovery from anaerobic gut microbes
Lazarina V. Butkovich, Oliver Vining, Michelle O'Malley
2025
DOI #: 10.1007 The animal gut microbiome is a complex system of diverse, predominantly anaerobic microbiota with secondary metabolite potential. These metabolites likely play roles in shaping microbial community membership and influencing animal host health. As such, novel secondary metabolites from gut microbes hold significant biotechnological and therapeutic interest. Despite their potential, gut microbes are largely untapped for secondary metabolites, with gut fungi and obligate anaerobes being particularly under-explored. To advance understanding of these… Read more
Methane evades microbes
David L. Valentine
2024
DOI #: 10.1038 Microbial activity in marine sediment acts as a barrier that generally prevents methane from escaping. However, a survey from the Baltic Sea suggests that in many locations the microbial population falters and methane can pass through freely.
From Trash to Treasure: Bioprospecting Nature’s Microbial Communities for Biotechnology
Michelle O'Malley
2024
Anaerobic microbes work together in complex communities that 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 build synthetic microbiomes to drive biomass to renewable chemicals. Herbivore fecal samples were challenged by different types of biomass during… Read more