Senior Scientist I/II, Microbial Strain Engineering

Flagship Pioneering•Cambridge, MA

3d•Onsite

About The Position

Flagship Pioneering is a bioplatform innovation company that invents and builds companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps. Those big leaps in human health, sustainability and beyond exponentially accelerate scientific progress in areas ranging from disease detection and treatment and nature-positive agriculture to novel applications of AI that are driving the creation of new technologies. What sets Flagship apart is our ability to advance science and technology by uniting innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform for the benefit of people and planet. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture. Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. THE ROLE We are seeking a Senior Scientist I or II to lead microbial strain engineering efforts to support a novel biological platform within one of Flagship Pioneering's stealth mode startups. This role will focus on designing, constructing, and optimizing engineered microbial strains to enable scalable production systems. The successful candidate will drive strain development cycles from genetic design through experimental validation, working closely with our discovery and bioprocess development teams to translate early biological insight into strains that perform robustly in fermentation environments. This individual will contribute technical leadership within the technical operations function and help establish best practices for microbial engineering within a collaborative and fast-moving R&D environment.

Requirements

PhD in microbiology, molecular biology, synthetic biology, microbial engineering, or related discipline
Scientist I: at least 5+ years of relevant experience in molecular or synthetic biology, with at least 2 years’ experience developing engineered microbial production strains
Scientist II: at least 8+ years of relevant experience in molecular or synthetic biology, with at least 4 years’ experience developing engineered microbial production strains
Demonstrated experience designing and executing microbial genetic engineering programs, including cloning, genome editing, or pathway engineering
Experience working with one or more microbial hosts such as bacteria, yeast, or filamentous fungi
Ability to independently design experiments, analyze results, and guide strain optimization strategies
Strong documentation and data management practices to ensure reproducibility and knowledge transfer

Nice To Haves

Experience engineering industrial microbial hosts such as E. coli, Bacillus, yeast, or filamentous fungal systems for protein secretion and display
Experience with modern DNA assembly and genome engineering techniques (e.g., Gibson assembly, Golden Gate, CRISPR-based editing)
Experience evaluating strain performance in microbial fermentation systems
Experience collaborating closely with bioprocess development teams to optimize strain performance in production environments
Experience working in startup or fast-paced R&D environments

Responsibilities

Design and implement microbial strain engineering strategies to improve production performance, stability, and robustness
Construct and evaluate engineered strains using modern molecular biology and microbial engineering techniques (e.g., genome editing, pathway optimization, promoter engineering)
Develop and execute iterative design-build-test-learn cycles to improve strain performance
Characterize engineered strains using appropriate analytical assays and collaborate with bioprocess teams to evaluate strain performance under fermentation conditions
Interpret experimental data and guide subsequent strain design decisions to advance production performance
Contribute to the development of strain engineering workflows, best practices, and experimental infrastructure within the organization
Mentor junior scientists or research associates and contribute to collaborative scientific planning