Senior Computational Microbiologist - 100%

Building the Future of Environmental Remediation

Join an innovative ETH spin-off dedicated to developing microbial solutions that degrade persistent environmental pollutants, including PFAS and pesticides. Our mission is to transition the world's first commercial bacterial solution for PFAS remediation from the laboratory to real-world industrial application. We are seeking a senior professional to establish and lead our in-house computational and molecular microbiology capability from the ground up.

Role Overview

This position bridges computation and experiment, offering the freedom and responsibility to shape data-inferred product development. You will establish a mechanistic and metabolic understanding of how bacterial strains and communities degrade PFAS and other persistent chemicals. This understanding will be translated into a computational pipeline that predicts strain performance and guides the rational design of synthetic microbial communities for specific use-cases. As a senior, high-impact, 100% onsite role, you will work hands-on with sequencing data from Illumina, Oxford Nanopore, and PacBio, as well as other omics and analytical data streams. You will also design experiments to validate computational predictions and supervise a Laboratory Technician supporting wet-lab and sequencing workflows.

Main Responsibilities

• Team Leadership & Supervision
  • Supervise and mentor the Laboratory Technician, coordinating wet-lab, cultivation, and sequencing workflows to ensure high-quality data for downstream analysis.
  • Set priorities and quality standards for sample preparation, sequencing, and data handover between the wet lab and bioinformatics.
• Bioinformatics Pipeline Development
  • Design, build, and maintain an in-house bioinformatics pipeline covering genome assembly, annotation, and comparative genomics from short-read and long-read sequencing data.
  • Evaluate and integrate the best available tools and methods, including AI/ML approaches, for genome mining, functional annotation, and strain characterization.
  • Ensure the pipeline is reproducible, scalable, and adaptable to incorporate new sequencing and omics data types as they become relevant.
• Metabolic Understanding & PFAS Degradation
  • Establish a metabolic-level understanding of how bacterial strains degrade PFAS, identifying the genes, enzymes, and pathways involved.
  • Build and apply genome-scale metabolic models to predict degradation capability and metabolic potential across strains.
• Experimental Validation & Strain Development
  • Design and run experiments, including genetic tools and functional assays, to validate predicted degradation genes and pathways.
  • Develop genetic tools for non-model environmental bacteria to support strain characterization and improvement.
• Predictive Modeling & Synthetic Community Design
  • Design and implement models that predict and learn from strain-level genomic and functional data to prioritize the most promising strains.
  • Develop a framework to guide the assembly of synthetic microbial communities per use case, based on predicted strain function and interaction potential.
• Collaboration, Field & Regulatory Support
  • Work closely with the R&D team to align bioinformatics outputs with experimental and pilot-project needs.
  • Monitor applied strains in pilot and field deployments.
  • Contribute technical documentation for regulatory and biosafety approval of microbial products.
  • Contribute bioinformatics analyses and insights to internal reports and, where relevant, client deliverables.

Your Profile

Required Qualifications

• PhD in Bioinformatics, Computational Biology, Microbial Genomics, or a related field.
• Senior-level experience (typically 5+ years) in microbiology research, combining computational and experimental work.
• Strong programming skills (Python and/or R) and experience with workflow managers (e.g., Nextflow, Snakemake).
• Hands-on experience applying AI/ML methods to biological or genomic data (e.g., function prediction, genome mining, metabolic modeling).
• Solid understanding of microbial physiology and metabolism, including enzymatic transformation and degradation pathways.
• Experience supervising, mentoring, or leading junior team members.
• Excellent English skills (C1 or higher).

Preferred Qualifications

• Direct experience in the PFAS field, or with biodegradation of other recalcitrant/xenobiotic pollutants.
• Experience designing or modeling synthetic microbial communities/consortia.
• Familiarity with long-read sequencing data (Oxford Nanopore, PacBio).
• Experience with regulatory documentation or field trials of applied microorganisms.
• Prior experience in a startup or applied biotech environment.

Note: Research indicates that women and individuals from marginalized groups tend to apply only when they meet all of the criteria. If you believe you are qualified, but do not necessarily check every box, please consider your fit for this role.

What We Offer

• A senior, high-impact role shaping the computational and molecular microbiology capability from the ground up.
• A cutting-edge scientific environment at the intersection of microbiology, genomics, and environmental biotechnology.
• Competitive salary and a stock option package.
• A collaborative startup culture with fast decision-making, a high level of responsibility, and the opportunity to shape the world's first commercial bacterial solution for PFAS remediation.