Acute Care Biobanking Core

The goals of the Acute Care Biobanking Core are to encourage and facilitate microbiome- focused research in the pathogenesis, diagnosis and treatment of patients with critical illness.  Many patients who are critically ill are subject to processes and complications with microbially-driven or infectious mechanisms.  The Core will assist in research by providing de-identified samples with linked clinical metadata to support research in this area, collect specimens as needed in support of microbiome research, and offer support for development of such research in the critical care setting.


(1) Provide a biobank of specimens that will be available “off the shelf” to enable studies of microbiome and critical illness,           with linked clinical metadata.         

           Specimens will be focused on critically ill subjects and specimens include

  • Upper respiratory tract
  • Lower respiratory tract
  • GI/Fecal

Linked but de-identified clinical metadata includes demographics, underlying & acute illnesses, antibiotics and other treatments, clinical microbiology data and extensive lab data.                                                                             
          Click here to see the specimens and samples available

 (2) Collect specimens & clinical metadata upon custom user request to assist with microbiome study implementation.

           The Core maintains clinical infrastructure in the critical care setting to collect specimens as needed upon user request,              as determined by goals of specific project and investigator needs. Specimen processing, logging and storage are                        available as well.

 (3) Assist with development of microbiome studies in the critical care setting for investigators new to the topic.
           The Core assists with study planning, preparation of IRB submissions, and other aspects of microbiome studies in the                critical care setting. 


Heat map representing lower respiratory tract bacterial communities of intubated subjects and healthy controls. 
Each column represents a single sample, and each row represents family-level taxonomic assignment of the sample’s 16S rRNA gene sequences. Vertical lines separate the 12 healthy controls (grouped to the left) and each of the intubated subjects (with serial sample from several). Modified from Kelly et al., Microbiome, 2016, 4:7.

Operational Information

Ronald Collman, MD
Core Director

Ayannah Fitzgerald, BSN
Clinical Coordinator

Layla Khatib, BS
Clinical Coordinator

Ize Imai
Core Technician

Please complete this form for study assistance and pricing information.


© The Trustees of the University of Pennsylvania | Site best viewed in a supported browser. | Site Design: PMACS Web Team.