Scientist II to Director: Microbiome Discovery & Colonization

Switch Bioworks; San Francisco (CA); On-site; USD 130,000 - 200,000; Full time

Job summary

Switch Bioworks is seeking a Scientist II to Director-level scientist to lead microbiome discovery and colonization efforts. You will design programs to identify variables governing root colonization, build consortia-assembly capabilities, and pair experimental microbiology with computational data science in a senior individual-contributor role with leadership scope.

You will mentor a small team, manage a large microbial biobank, and collaborate with engineering, field, and process teams to move

Qualifications

• Ph.D. in Microbiology or related field; 5+ years post-PhD industry R&D experience developing microbial products.
• Experience leading discovery programs and translating data into actionable candidates.
• Strong computational and data-science fluency with ability to build predictive frameworks.

Responsibilities

• Define and lead scientific programs to discover, characterize, and deploy microbial consortia for host environments, starting with corn root microbiome.
• Build and manage a large microbial biobank with provenance and chain-of-custody.
• Develop quantitative colonization metrics and translate measurements into practice; design and execute consortia-assembly campaigns.
• Lead cross-functional collaboration with engineering, field, and process teams to move winners toward field deployment.
• Mentor scientists and research associates; set technical direction and contribute to planning and budgeting.

Skills

Experimental microbiology

Computational biology

Data analysis

Cross-functional leadership

Mentoring/people leadership

Education

Ph.D. in Microbiology or related discipline

Tools

Bioinformatics tools

High-throughput workflows

Job description

Scientist II to Director: Microbiome Discovery & Colonization

This role is level-agnostic. We are hiring the right person across the Scientist–Director range and will calibrate title, level, and scope to prior experience.

About Switch Bioworks

Based in San Carlos, CA, Switch Bioworks is redefining bioproduction through programmable microbes. Beginning with agriculture, we are developing nitrogen-fixing microbial consortia that live directly on crop roots. This replaces expensive, carbon-intensive synthetic fertilizers with a living alternative that reshapes the economics and sustainability of farming.

Our edge lies in our namesake “switches” - synthetic biology control systems that activate microbial production only when and where it’s needed. By combining microbial ecology with advanced genetic control systems, Switch is building a biological platform with the potential to transform agriculture and a wide range of industrial bioproduction applications.

Learn more at www.switchbioworks.com

About the position

You will own Switch's effort to discover, characterize, and deploy consortia of microbes that reliably establish in the host environment, starting with the corn root microbiome and building a platform extensible to other microbiomes over time.

Competitive colonization is a big challenge for the field, and advancing it is the central mandate of this role. We need a thought leader to design scientific programs that identify the variables that govern root colonization and systematically build consortia-assembly capability that combines bioinformatic and experimental evidence into confident strain-prioritization decisions.

We are looking for a hands-on scientific leader who pairs deep experimental microbiology with strong computational and data-science instincts. This is a senior individual-contributor role with people-leadership scope. You will be at the bench routinely designing, running, and troubleshooting experiments yourself and mentoring a small team directly or cross-functionally. You will build and mine a large microbial biobank as our discovery engine, run discovery and consortia assembly campaigns, establish rigorous quantitative colonization measurements, and partner closely with our engineering, field, and process teams to move winners toward the field.

Objectives and responsibilities

• Colonization & Microbiome Performance: Define and hit quantitative colonization targets, starting with the corn root microbiome and expanding into new microbiome fields over time. Design and lead the scientific program to identify the governing variables and systematically build a consortia-assembly capability that integrates bioinformatic and experimental data.


• Biobank Development: Build, curate, and mine a large, well-characterized microbial biobank spanning culturomics, structured metadata capture, and storage powered by automated, high-throughput workflows across isolation, phenotyping, and screening that scale strain characterization and compress discovery-to-prioritization cycle times. Establish documented provenance and chain of custody for every isolate from the point of collection to handoff to the engineering team.


• Quantitative Microbiology & Data Science: Establish rigorous colonization quantification methods and own the translation of measurements from grow room/greenhouse systems into the field. Analyze complex sequencing and phenotyping datasets, and build reproducible bioinformatic and computational workflows that guide isolation, strain prioritization, and consortia design.


• Consortia Design & Predictive Modeling: Design and assemble multi-strain consortia with manufacturing reality from the outset. Build predictive models that link strain traits and interactions to colonization and function initially optimized for corn roots, with a framework extensible to additional crops or different microbiome systems over time including the human gut microbiome.


• Intellectual Property: Recognize patentable inventions as they emerge from the microbiome discovery efforts and contribute to invention disclosures.


• Trial & Cross-functional Support: Partner with the engineering, field, and process teams to validate colonization; support growth chamber, greenhouse, and field studies with well-characterized materials and analysis.


• Team & Mentorship: Support, mentor, and guide a small team of scientists and research associates through direct and indirect influence. Set day-to-day technical direction for the group, guide people development, contribute to headcount and spend planning, and manage project budgets and external services.

Characteristics of a successful candidate

• Must be authorized to work full-time in the U.S. and able to work on-site daily in San Carlos, CA.


• Deep experimental microbiology mastery, including microbial isolation, culturing, and plant-microbe colonization assays.


• Computational and data-science fluency; ability to set analytical standards, critically interrogate sequencing and phenotypic datasets, and translate results into strain-prioritization decisions in close partnership with other teams.


• At least 5 years of post-PhD industry R&D experience developing microbial products, ideally closer to 10. A track record of moving microbial candidates through an industrial discovery pipeline while staying close to the science.


• Demonstrated success building and curating microbial culture collections (biobanks) using high-throughput approaches, and translating discovery pipelines into prioritized, testable candidates — including the metadata, provenance, and chain-of-custody practices that make a biobank a durable asset.


• A systematic program-builder: able to look at an open problem like colonization, identify the variables that matter, and stand up the assembly-and-screening capability to work through them methodically, combining bioinformatics and experimental data.


• Comfort working across biological systems: able to establish rigor in the corn root microbiome and carry those methods and frameworks into new applications and verticals as the platform expands.


• Strong interpersonal and cross-functional leadership skills; able to bridge experimental biology, data science, engineering, and field application.


• Experience mentoring or supervising scientists and associates, and the appetite to grow a small team.


• An "owner" mindset with the ability to drive independent projects in a fast-paced startup environment, design rigorous experiments, interpret complex data, and influence across the organization.


• A mission-driven team player and "culture-carrier" eager to collaborate across diverse teams.

Preferred Qualifications

• Ph.D. in Microbiology, Plant‑Microbe Interactions, Microbial Ecology, Soil Science, Bioinformatics, or a related discipline.


• Expertise in AI/ML, computational biology, bioinformatics, and statistical/data-science methods applied to sequencing and phenotypic datasets.


• Experience developing or working with commercialized microbial products in agriculture, including exposure to EPA/USDA regulatory requirements.


• Experience across two or more microbiome verticals: agricultural/plant and gut/human considered a significant asset; agricultural/rhizosphere and root-associated microbial ecology preferred.

Expected salary range

$130,000 - $200,000 Salary and Title commensurate with experience. Switch Bioworks is an equal opportunity employer.