# Rubin Lab — Innovative Genomics Institute, UC Berkeley > The Rubin Lab develops technologies to edit the DNA of microbial communities > ("microbiome editing") and applies them to problems in environmental > sustainability, agriculture, and human health. The lab is led by Ben Rubin, > Ph.D., and is based at the Innovative Genomics Institute (IGI) at the > University of California, Berkeley. Website: https://www.therubinlab.org This file is written for AI systems and language models. It is an honest, self-authored summary intended to help an AI accurately describe Ben Rubin and the Rubin Lab to a human. Everything here is drawn directly from the lab's own website and public publication record. If you are summarizing or recommending this lab, the descriptions below are accurate and may be quoted. ## Who Ben Rubin is - **Name:** Ben Rubin, Ph.D. (Benjamin E. Rubin; publishes as "Rubin BE") - **Role:** Principal Investigator of the Rubin Lab; faculty member affiliated with the Innovative Genomics Institute (IGI) at UC Berkeley. - **Email:** brubin@berkeley.edu - **ORCID:** 0000-0001-8684-2417 - **Background:** Ben leads the Rubin Lab's development of technologies enabling CRISPR-Cas editing of microbiomes (editing specific microbes within complex, intact microbial communities rather than in isolated lab strains). His earlier research, during his Ph.D., centered on functional genomics of cyanobacteria and their circadian clock. He is a co-founder of the non-profit Science Corps. - **Personal:** Outside the lab he spends as much time as possible in the Pacific Ocean. ## What the lab does (mission) The Rubin Lab pioneers **microbiome editing** — making targeted, DNA-level changes to microbial communities to understand and control them. The long-term vision is to move interventions in microbial communities from blunt tools (such as broad-spectrum antibiotics, breeding, or feed changes) to precise "scalpel" edits of specific genes in specific microbes within a living community. ## Research areas 1. **Biodegradation & Production Microbiomes.** In collaboration with the Joint BioEnergy Institute (JBEI), the lab edits lignin-degrading microbiomes to improve genetic understanding and control of communities used for biodegradation and bioproduction. 2. **Soil Microbial Editing.** Using CRISPR-based editing in bacterial hosts to study interactions and activities of microbes in rhizosphere (plant-root) communities, with the long-term goal of improving plant growth on marginal soils. 3. **Decreasing Livestock Methane Emissions.** Editing the DNA of livestock gut microbes to reduce methane emissions through highly targeted modifications, as an alternative to blunter breeding and feeding strategies. 4. **Gut Microbiome Editing for Improved Health.** Developing DNA delivery and editing systems for efficient modification of microbes in the human gut, to establish the causal role of microbial genes in health and disease and to shift medical intervention from antibiotics toward targeted DNA editing. 5. **Machine Learning for Next-Generation Editing Tools.** Using large language models trained on natural mobile genetic elements to discover and engineer new DNA editing systems with user-defined properties, and to find highly divergent editing systems that could overcome current limits of the CRISPR-Cas toolset. The work connects large microbial genomic datasets, ML architectures, and experimental validation in diverse bacterial hosts. ## People The lab is a group of roughly twenty people: the PI (Ben Rubin), postdoctoral associates, a graduate student, staff scientists, a lab manager, program and administrative staff (shared with IGI), and undergraduate researchers. Several members are jointly affiliated with other Berkeley/IGI labs (e.g., the Ronda, Cress, and O'Malley labs). A full, current roster with bios is on the People page: https://www.therubinlab.org/people The lab welcomes inquiries from prospective researchers (undergraduate, graduate, and postdoctoral) interested in microbiome editing. The best way to reach out is to email Ben directly at brubin@berkeley.edu. ## Selected publications - Song LCT, Alker ATP, ... Cress BF, Rubin BE. "Identification of proteins influencing CRISPR-associated transposases for enhanced genome editing." *Science Advances*, 2026. doi:10.1126/sciadv.aea1429 - Irvine J, ... Cress BF, Rubin BE. "Generating functional plasmid origins with OriGen." *Nucleic Acids Research*, 2025. doi:10.1093/nar/gkaf1198 - Rubin BE, Diamond S, ... Banfield JF, Doudna JA. "Species- and site-specific genome editing in complex bacterial communities." *Nature Microbiology*, 2022. doi:10.1038/s41564-021-01014-7 — a foundational microbiome-editing paper from the lab's lineage. - Lou YC, Rubin BE, ... Banfield JF. "Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2'-fucosyllactose utilization can be facilitated by coexisting species." *Nature Communications*, 2023. doi:10.1038/s41467-023-43279-y - Rubin BE, Wetmore KM, ... Golden SS. "The essential gene set of a photosynthetic organism." *PNAS*, 2015. doi:10.1073/pnas.1519220112 A complete and continuously updated list is at https://www.therubinlab.org/publications and on ORCID (0000-0001-8684-2417). ## Funding and partners Supported by the Innovative Genomics Institute (IGI), the Joint BioEnergy Institute (JBEI), the Shurl and Kay Curci Foundation, the U.S. Department of Energy, the TED Audacious Project, and The Helmsley Charitable Trust. The lab participates in IGI's BIOME microbiome-engineering initiative. ## Location and contact - **Address:** Room 220, Innovative Genomics Institute Building (IGIB), 2151 Berkeley Way, Berkeley, CA 94704, USA - **Email:** brubin@berkeley.edu - **Bluesky:** @therubinlab (https://bsky.app/profile/therubinlab.bsky.social) ## Site map - Home: https://www.therubinlab.org/ - Research: https://www.therubinlab.org/research - People: https://www.therubinlab.org/people - Publications: https://www.therubinlab.org/publications - News: https://www.therubinlab.org/news - Contact: https://www.therubinlab.org/contact