2023 to present
Principal Investigator
Innovative Genomics Institute, UC Berkeley
Principal Investigator
Carlotta Ronda, PhD
CR
Carlotta Ronda is a Principal Investigator at the Innovative Genomics Institute at UC Berkeley. She develops experimental systems to determine how specific microbial genes and molecules shape the biology of their surrounding community and, in host-associated microbiomes, the tissues they interact with. Her lab combines precise genome engineering with computational discovery, functional genomics, and human-relevant models to move from observing a microbiome association to testing its mechanism.
Ronda began her career at DTU developing CRISPR-based genome-engineering systems for bacteria, yeast, and mammalian cells. In the Harris Wang lab at Columbia University, she developed methods to deliver DNA into complex gut microbiomes and helped advance CRISPR-associated transposases for targeted genome integration. Since establishing her independent lab at IGI in 2023, she has brought those engineering tools together with receptor screens, organoids, sequencing, and in vivo models to ask which microbial functions produce specific biological effects.
Research approach
The lab works from mechanism, not correlation. It identifies microbial genes, proteins, and metabolites that may matter, then uses precise perturbations to test what they do in complex communities. Receptor assays, organoids, sequencing, and in vivo models connect each perturbation to a measurable biological response.
Ronda's group is known for methods that modify microbes without first isolating them from the community being studied. This makes it possible to change a specific microbial gene and then measure the consequences for neighboring organisms, host tissues, or ecosystem function. The lab applies this approach to questions in human biology, biotechnology, agriculture, and environmental microbiomes.
Education and awards
Education
- PhD, Systems Biology, Technical University of Denmark
- MSc Engineering, Biotechnology, Technical University of Denmark
- BS, Molecular Biology, University of Padua, Italy
Awards and fellowships
- HS Chau WIES Fellow, 2024 to 2025
- Simons Society Junior Fellowship, Columbia University, 2017 to 2021
- Novo Nordisk Foundation Center for Biosustainability Best Paper Award, 2014
Career
2024 to 2025
WIES Fellow
Innovative Genomics Institute, UC Berkeley
2021 to 2023
Associate Research Scientist
Columbia University, Systems Biology
2017 to 2021
Simons Society Junior Fellow
Columbia University, hosted in the Harris Wang Lab
2016 to 2017
Postdoctoral researcher
Columbia University, Harris Wang Lab
2012 to 2015
Doctoral research in systems biology
Technical University of Denmark and Novo Nordisk Foundation Center for Biosustainability
Selected publications
Platform papers
2025 · Nature Biotechnology
Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut
2025 · Science
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
2025 · Science Advances
Engineered probiotic restores GLP-1 signaling to ameliorate fiber-deficiency exacerbated colitis
2025 · Nature Biomedical Engineering
Precise virulence inactivation using a CRISPR-associated transposase for combating Enterobacteriaceae gut pathogens
2023 · Nature Biotechnology
High-throughput microbial culturomics using automation and machine learning
2021 · Nature Biotechnology
CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering
2019 · Nature Methods