Fermentation Engineer at Whole Biome
San Francisco, CA, US

Whole Biome is a ground-breaking biotechnology company, backed by blue-chip investors, that is developing and commercializing products to address key chronic diseases using proprietary technologies to understand and target the human microbiome. Whole Biome has created a unique discovery platform to identify key, novel bacterial strains and the prebiotics that feed them to develop Live SynbioticsTM, products that augment a person’s microbiome. We are a small team of scientists, engineers and physicians interested in improving human health by using the latest research from diverse fields, such as, microbiology, molecular biology, high-throughput genomics, distributed computing, pharmaceutical development and nutrition sciences.

The Manufacturing team is seeking a Fermentation Engineer to lead the  development and optimization of the company’s microbial fermentation processes for the production of microbiome interventions. This individual should be well-versed in fermentation science, fermentation equipment, process development/optimization/control, validation testing, and cGMP practices. Additionally, the ideal candidate will have a good understanding of microbial physiology, secondary metabolism and biosynthetic pathways. The individual should take into consideration scalability of the upstream and downstream process from laboratory scale to manufacturing scale. We are seeking an energetic, creative, and highly self-motivated individual that enjoys challenges in fermentation development and working closely in a team of manufacturing associates and microbiologists. The successful candidate will also interact closely with a cross-functional team of Molecular Biologists, Statisticians, Operations and Product Marketing.


  • Design and analyze fermentation experiments to maximize understanding and performance of strains and meet project goals for yield, productivity, purity specifications, and other process parameters
  • Optimize fermentation processes and apply new process technologies and strategies at manufacturing scales under food cGMP guidelines
  • Help expand the fermentation group and advise the design of a new fully functional fermentation facility
  • Collaborate with operations team and fellow process development scientists to ensure that experiments are designed and executed effectively
  • Communicate with internal and external stakeholders through meetings and clearly written emails, reports and presentations
  • Responsible for individual and co-worker safety
  • Building automated solutions to improve fermentation operation workflows under GMP requirements
  • Develop new high throughput plate-based assays to use across a variety of microbes


  • Minimum of 3 years experience in up- and downstream bioprocess development, and  designing and analyzing fermentation experiments for strain screening and scale-up
  • Experience in operating lab-scale bioreactors and bioprocesses
  • Proficient in physiological and functional strain characterization at bench scale and microtiter-plate scale
  • Experience using design of experiment (DoE) methodology for optimization and characterization of fermentation processes
  • Experience in scale-up fermentation processes from bench scale to pilot scale
  • Ability to work well in a fast-paced environment and handle multiple projects simultaneously
  • Demonstrated strong project management, organization, facilitation, problem solving, and quantitative analysis skills
  • Ability to communicate technical results and challenges clearly and effectively to colleagues and managers, in written and verbal formats
  • Anaerobic microbial fermentation experience strongly preferred
  • Experience with food or biopharma cGMP manufacturing
  • An outstanding team player with a positive attitude
  • Ability to stand or sit for prolonged periods, climb, kneel, bend, and at times lift objects as heavy as 50 lbs

​Email with your resume and cover letter to begin the application process.  Even if you don't see an opening that fits you, please send us your resume if you think your background and personality would be a great fit!


  •  competitive salary and equity packages
  •  health, dental, and vision
  •  401k with corporate matching
  •  flexible schedules with a focus on work/life balance
  • unlimited vacation policy (we're all adults and professionals, not clockwatchers)
  • commuter benefits

Sweet Perks

  •  casual culture (66% of founders usually wearing hoodies)  
  • ​ on-site gym
  •  work/life balance: we believe it, we encourage it, we live it
  •  collaborative, team environment
  •  off-site, team building adventures
  •  walking distance to Caltrain, Muni
  •  walking distance to bars and restaurants in Dogpatch