A5034689787- Gut microbiota and health
- CRISPR and Genetic Engineering
- Evolutionary Game Theory and Cooperation
- Evolution and Genetic Dynamics
- 3D Printing in Biomedical Research
- Clostridium difficile and Clostridium perfringens research
- Cancer Cells and Metastasis
- Escherichia coli research studies
- Plant and animal studies
- Epigenetics and DNA Methylation
- Microscopic Colitis
- Cystic Fibrosis Research Advances
- Genomics and Phylogenetic Studies
- Modular Robots and Swarm Intelligence
- Microfluidic and Bio-sensing Technologies
- Antibiotic Resistance in Bacteria
- Viral gastroenteritis research and epidemiology
- Protist diversity and phylogeny
- Enterobacteriaceae and Cronobacter Research
University of California, Berkeley
2025
Innovative Genomics Institute
2025
Montana State University
2015-2023
University of Minnesota
2021-2023
Biotechnology Institute
2021-2023
Abstract Longitudinal human gut microbiome datasets generated using community-level, sequence-based approaches often report a sub-set of long-lived “resident” taxa that rarely, if ever, are lost. This result contrasts with population-level turnover resident clones on the order months to years. We hypothesized disconnect between these results is due relative lack simultaneous discrimination at both community and population-levels. Here, we present small, longitudinal cohort study (n = 8...
ABSTRACT Clostridium difficile is the most commonly identified pathogen among health care-associated infections in United States. There a need for accurate and low-cost typing tools that produce comparable data across studies (i.e., portable data) to help characterize isolates during epidemiologic investigations of C. outbreaks sporadic cases disease. The popular -typing technique PCR ribotyping, we previously developed methods using fluorescent primers amplicon sizing on Sanger-style...
Mutually beneficial interspecific interactions are abundant throughout the natural world, including between microbes. Mutualisms microbes critical for everything from human health to global nutrient cycling. Studying model microbial mutualisms in laboratory enables highly controlled experiments developing and testing evolutionary ecological hypotheses. In this review, we begin by describing tools available studying mutualisms. We then outline recent insights that systems have shed on...
While generative artificial intelligence (AI) has shown promise for biological design, no computational system yet created and validated sequences capable of autonomous replication. Focusing on plasmids, one the smallest types replicating elements, we develop OriGen, a sequence model that generates new plasmid origins replication while maintaining key elements essential their We experimentally validate OriGen's ability to create functional diverge from existing wild types, demonstrating...
Predicting evolution in microbial communities is critical for problems from human health to global nutrient cycling. Understanding how species interactions impact the distribution of fitness effects a focal population would enhance our ability predict evolution. Specifically, does type ecological interaction, such as mutualism or competition, change average effect mutation (i.e., mean effects)? Furthermore, often increasing community complexity alter on mutant fitness? To address these...
CRISPR-Associated Transposases (CASTs) hold tremendous potential for microbial genome editing due to their ability integrate large DNA cargos in a programmable and site-specific manner. However, the widespread application of CASTs has been hindered by low efficiency diverse, non-model bacteria. In an effort address this shortcoming, we conducted first genome-wide screen host factors impacting Vibrio cholerae CAST (VchCAST) activity used findings increase VchCAST efficiency. A...
Abstract Despite extensive literature on the pathogenicity and virulence of opportunistic pathogen Escherichia coli , much less is known about its ecological evolutionary dynamics as a commensal in healthy hosts. Based two detailed longitudinal datasets gut microbiota adult individuals followed over months to years France USA, we identified robust trade-off between ability establish new host (colonization) remain (residence). Major E. lineages (phylogroups) exhibited similar fitness but...
Predicting evolution in microbial communities is critical for problems from human health to global nutrient cycling. Understanding how species interactions impact the distribution of fitness effects a focal population would enhance our ability predict evolution. Specifically, it be useful know if type ecological interaction, such as mutualism or competition, changes average effect mutation (i.e., mean effects). Furthermore, often does increasing community complexity alter on mutant fitness?...