Senior Scientist I/II, Microbial Strain Engineering

COMPANY DESCRIPTION

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.

KEY 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

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• 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

PREFERRED EXPERIENCE

• 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

LOCATION:  Cambridge, MA

ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies 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. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

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The salary range for this role is $126,000 - $181,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Protocos currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Protocos's good faith estimate as of the date of publication and may be modified in the future.