Shedd Aquarium seeks a Postdoctoral Analyst to join a multi-disciplinary research group examining the role of the environmental microbiome in disease prevention for aquarium animals. The individual will use their understanding of principles governing microbial community assembly and function to provide analysis and interpretation of amplicon sequence data and metagenomic data sets. In addition, the individual will be responsible for developing, refining and implementing bioinformatics pipelines and preparing results for dissemination. The Postdoctoral Analyst directly supports activities under IMLS National Leadership Grant MG-60-18-0018-18 as well as ongoing investigations driven by the Aquarium and its external partners. By applying expertise in microbial ecology to data from engineered aquatic systems and exotic species, the Postdoctoral Analyst will have opportunity to inform management decisions made not only by Shedd Aquarium but by institutional peers, regulatory agencies and conservation organizations.

Microbial ecology research at Shedd Aquarium is overseen by the A. Watson Armour Center for Animal Health under Center Director and VP William Van Bonn, DVM. Projects are reviewed by a Science Advisory Group which includes representatives of diverse stakeholders including USDA, University of Chicago/Microbiome Center and Sea World. Collaborative studies are ongoing with Jack Gilbert (University of Chicago/Argonne National Labs), Angela Kent (University of Illinois at Urbana-Champaign), Joan Rose (Michigan State University) and Lut Raskin (University of Michigan). For a complete list of publications and projects visit

The position is based at Shedd Aquarium’s onsite molecular and microbial ecology laboratory with capacity including high-throughput DNA and RNA purification, sequencing on the Illumina MiSeq platform and real-time PCR. Access to a High Performance Computing Cluster is available. Successful candidates will be team players with a strong publication record who share our passion for helping animals.

This position is a 2-year term, with extension possible pending performance.

Duties & Responsibilities:

  • Demonstrate commitment to Shedd’s vision, mission and values.
  • Analyze next-generation sequence data to characterize microbial community dynamics and functional capacity.
  • Develop, execute and improve analytical pipelines based on evaluation of bioinformatic tools and reference databases.
  • Interpret results, articulate conclusions and assist in formulating new hypotheses as part of a collaborative, multi-disciplinary team.
  • Prepare findings for dissemination in peer-reviewed publications.
  • Assist in reviewing research proposals from prospective collaborators, contributing knowledge of microbial community analysis and studydesign.
  • Present research findings at scientific and professional conferences. Deliver informal presentations to Aquarium leadership and staff.
  • Participate as-needed in educational and outreach activities aimed at providing authentic science experiences to teens, undergraduates and adults.
  • Demonstrate a commitment to professional and personal growth by initiating dialogue with colleagues, engaging in self-directed learning and focusing on professional development goals.
  • Fulfill other duties as required.



  • Ph.D. in microbiology, microbial ecology, environmental engineering, or other relevant field.


  • Experience using genomic approaches to identify and characterize microbial assemblages, including 16S rRNA gene profiling and shotgun metagenomics. Experience with ITS/18S a plus.
  • Familiarity with analysis methods utilizing bioinformatic tools/databases such as mothur, QIIME/QIIME2, Greengenes, RDP, SILVA and phyloseq. Understanding of gene, protein and pathway annotations.
  • Proficient in using python or R for microbial community bioinformatics and experience with code version control systems such as Git.
  • Understanding of how to select and apply appropriate statistical methods.
  • Experience with Linux-based HPC clusters.
  • Record of primary contributions to peer-reviewed publications. 
  • Strong quantitative and analytical skills.
  • Outstanding written and oral communication skills.
  • Demonstrated ability to collaborate with diverse teams in a professional setting.

Designations/Certifications: Membership in relevant professional societies such as American Society for Microbiology or International Society forMicrobial Ecology preferred.

Application deadline: Open until filled
Start date:
Location: Chicago, IL