Principal Scientist GMP Microbiology Lilly Medicine Foundry

Lilly recently announced a $4.5 billion investment to create the Lilly Medicine Foundry — the first-ever facility to combine research and manufacturing in a single location, expanding capacity for clinical trial medicines while reducing costs and environmental impact. 

Analytical GMP Laboratories (AGL) supports GMP testing across the Lilly Medicine Foundry (LMF) and the broader Product Research & Development (PRD) network, spanning environmental monitoring, microbiology, GMP testing, raw materials, and cleaning/investigations. AGL sits at the intersection of science and quality — this role offers the opportunity to shape the analytical compliance program from the ground up and help drive quality culture at a cutting-edge facility. 

The Principal Scientist, GMP QC Microbiology is the subject matter expert supporting the Sr. Advisor of Env. Monitoring & Microbiology in day-to-day microbiological testing and batch disposition for clinical GMP manufacturing at the Medicine Foundry Analytical GMP Laboratory. The role executes and oversees compendial and non-compendial microbiological testing including sterility, bioburden, endotoxin (Bacterial Endotoxin Test), microbial limits, and water testing; leads laboratory investigations; authors change controls and SOPs; and trains and mentors junior analysts. Partnering with the Sr. Advisor, Quality Assurance, Manufacturing, and Regulatory Affairs, the role contributes to method validation and inspection readiness in compliance with cGMP, data integrity (ALCOA+),  EU GMP Annex 1, and applicable global regulatory requirements. 

What You'll Do 

Testing & batch disposition 

• Perform and oversee sterility, bioburden, microbial limits, and water system testing; serve as primary data reviewer for accurate and timely batch disposition. 

• Perform microbial identification testing and maintain the site isolate library; support EM activities as back-up coverage. 

Method validation & change control 

• Lead method validations, transfers, and verifications; prepare protocols and summary reports and author change controls for test methods, specifications, and SOPs. 

• Support qualification of laboratory equipment and evaluate new rapid microbiological methods (RMM). 

Investigations, OOS & CAPA 

• Lead OOS/OOT and other laboratory investigations; author deviation reports and drive CAPA to closure with QA. 

Regulatory compliance & audit readiness 

• Maintain documentation in a state of inspection readiness, serve as SME during inspections and audits, and support remediation of audit observations to closure. 

• Stay current on applicable compendial standards and regulatory requirements; update SOPs to reflect evolving requirements. 

Training, mentorship & continuous improvement 

• Develop and deliver training for junior analysts on test methods, aseptic technique, and cGMP; serve as a qualified trainer; and maintain training records and competency matrices. 

• Partner with the Advisor on lab workflow and continuous improvement initiatives. Handle biohazardous and hazardous materials per EHS requirements. 

Safety and GMP execution  

• Ensure laboratory, cleanroom, and manufacturing support activities are performed safely and in accordance with approved procedures, cleanroom behaviors, and GMP expectations. 

Minimum Qualifications 

• BS or MS in in Microbiology, Biology, Biochemistry, Pharmaceutical Sciences, or related technical discipline 

• BS with 5+ years or MS with 3+ years of experience in cGMP pharmaceutical microbiology experience, including compendial method execution, investigation authoring, and analyst mentoring. 

• Equivalent combinations of education and cGMP microbiology experience will be considered. 

Additional Skills and Preferences 

• Experience with aseptic manufacturing or sterile drug product operations (fill–finish, lyophilization). 

• Proficiency with EM data systems including MODA, LabVantage, Metasys, and quality management systems (TrackWise, Veeva Vault). 

• Experience with RMM platforms (BacT/ALERT, Bactec, Milliflex, NAT/PCR sterility). Prior work with LIMS, ELN, LabVantage, TrackWise, or Veeva Vault.  

• Working knowledge of microbial identification techniques (MALDI-TOF, Vitek, Gram stain). 

• Experience working in a greenfield or start-up laboratory environment, including contributing to lab build-out, SOP authoring from scratch, equipment selection and qualification, and establishing a quality culture from the ground up. 

Additional Information 

• Location: Initial location at Parkwood West, Carmel, IN, with occasional work at Lilly Technology Center, Indianapolis. Permanent location at the Lilly Medicine Foundry in Lebanon, IN. 

• Travel: Less than 5% domestic 

• Regular work in controlled cleanroom environments (ISO 5–8 / Grade A–D) requiring gowning per applicable SOP requirements. 

• May require occasional off-hours, weekend, or on-call availability to support critical manufacturing campaigns or investigation response. 

• Physical requirements include standing for extended periods, walking throughout the facility, and performing gowning activities.