About

Eric Gerd Pamer, MD, is the Donald F. Steiner Professor of Medicine at the University of Chicago, where he also holds positions as Professor of Microbiology and Professor of Pathology. He is actively involved in multiple committees including the Committee on Cancer Biology, the Committee on Clinical Pharmacology and Pharmacogenomics, and the Committee on Immunology. Dr. Pamer is the Director of the Duchossois Family Institute. His research focuses on host-pathogen interactions, infectious diseases, microbiology, microbiome, and microbiota. His laboratory studies interactions between pathogenic and beneficial bacteria and their mammalian hosts, utilizing genomic, proteomic, and metabolomic approaches, and employs gnotobiotic mice to test commensal consortia for their ability to enhance resistance against pathogenic bacteria. His work has identified novel mechanisms of antimicrobial resistance that can be exploited to reduce infection risks from highly antibiotic-resistant pathogens. Additionally, he has collaborated with clinical groups to investigate the microbiota's role in clinical outcomes, demonstrating that loss of microbiota diversity impacts outcomes during allogeneic hematopoietic cell transplantation and influences the risk of colitis during checkpoint blockade cancer immunotherapy. Dr. Pamer's educational background includes an MD from Case Western School of Medicine and a BA in Biology from Case Western Reserve University. His research has contributed significantly to understanding the microbiota's role in health and disease, with numerous publications in high-impact journals.

Research topics

• Biology
• Microbiology
• Medicine
• Immunology
• Bioinformatics
• Internal medicine
• Gastroenterology
• Genetics
• Biochemistry
• Ecology
• Physiology
• Pathology
• Endocrinology
• Computational biology
• Biotechnology

Selected publications

• Code and knowledgebase data for "IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry"

  Open MIND · 2026-05-06

  datasetOpen access

  About This repository contains the complete codebase and infrastructure for the IDBac platform, a centralized knowledgebase and analysis system for bacterial dereplication using MALDI-TOF mass spectrometry protein signatures. Please note: While the current IDBac knowledgebase contains version 4.2 of the RKI database, the JSON file listed here intentionally excludes this. Please find the source data for RKI used in the publication here. Abstract The identification of bacteria is central to microbiological sciences. While gene sequencing methods have been the standard to identify bacteria, use of MALDI-TOF mass spectrometry (MS) in clinical microbiology provides high-throughput identification to the subspecies level. However, biotyping has yet to be adopted outside of clinical microbiology due to the lack of a centralized public database of MS protein signatures that would facilitate strain identification via spectral comparison. Herein we present the IDBac web platform, a crowd-sourced central knowledgebase of protein MS signatures of >1400 strains spanning 6 bacterial phyla. Accompanying the knowledgebase is analysis infrastructure to identify unknown isolates, probe relationships within culture collections, and visualize specialized metabolite differences within groups of closely related bacteria. We highlight this utility by demonstrating the dereplication of bacterial isolates using the seed knowledgebase, identifying trends in culture collections using metadata integration, and reporting the discovery of a new metabolite from a Paraburkholderia isolate.

  PublisherDOI

• Code and knowledgebase data for "IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry"

  Zenodo (CERN European Organization for Nuclear Research) · 2026-05-06

  datasetOpen access

  About This repository contains the complete codebase and infrastructure for the IDBac platform, a centralized knowledgebase and analysis system for bacterial dereplication using MALDI-TOF mass spectrometry protein signatures. Please note: While the current IDBac knowledgebase contains version 4.2 of the RKI database, the JSON file listed here intentionally excludes this. Please find the source data for RKI used in the publication here. Abstract The identification of bacteria is central to microbiological sciences. While gene sequencing methods have been the standard to identify bacteria, use of MALDI-TOF mass spectrometry (MS) in clinical microbiology provides high-throughput identification to the subspecies level. However, biotyping has yet to be adopted outside of clinical microbiology due to the lack of a centralized public database of MS protein signatures that would facilitate strain identification via spectral comparison. Herein we present the IDBac web platform, a crowd-sourced central knowledgebase of protein MS signatures of >1400 strains spanning 6 bacterial phyla. Accompanying the knowledgebase is analysis infrastructure to identify unknown isolates, probe relationships within culture collections, and visualize specialized metabolite differences within groups of closely related bacteria. We highlight this utility by demonstrating the dereplication of bacterial isolates using the seed knowledgebase, identifying trends in culture collections using metadata integration, and reporting the discovery of a new metabolite from a Paraburkholderia isolate.

  PublisherDOI

• Table S1 from Dietary Fiber Lacks a Consistent Effect on Immune Checkpoint Blockade Efficacy Across Diverse Murine Tumor Models

  2025-09-25

  articleOpen access

  <p>Details of experimental diets</p>

  PublisherDOI

• Figure S3 from Dietary Fiber Lacks a Consistent Effect on Immune Checkpoint Blockade Efficacy Across Diverse Murine Tumor Models

  2025-09-25

  articleOpen access

  <p>Extended serum and fecal metabolomic analyses in the different tumor models</p>

  PublisherOA PDFDOI

• Table S9 from Dietary Fiber Lacks a Consistent Effect on Immune Checkpoint Blockade Efficacy Across Diverse Murine Tumor Models

  2025-09-25

  articleOpen access

  <p>Fecal metabolite peak areas from the B16-OVA model</p>

  PublisherDOI

• Table S6 from Dietary Fiber Lacks a Consistent Effect on Immune Checkpoint Blockade Efficacy Across Diverse Murine Tumor Models

  2025-09-25

  articleOpen access

  <p>Serum metabolite peak areas from the YUMM1.1-9 model</p>

  PublisherDOI

• Figure S1 from Dietary Fiber Lacks a Consistent Effect on Immune Checkpoint Blockade Efficacy Across Diverse Murine Tumor Models

  2025-09-25

  articleOpen access

  <p>Flow cytometry gating strategy</p>

  PublisherOA PDFDOI

• IDBac: an open-access web platform to identify bacteria and analyze relationships in culture collections using MALDI-TOF mass spectrometry

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-15

  preprintOpen access

  Abstract The identification and analysis of bacteria is central to the microbiological sciences. While gene sequencing methods have been the standard to achieve this, use of MALDI-TOF mass spectrometry (MS), particularly in clinical microbiology, provides high-throughput identification to the subspecies level. However, biotyping has yet to be adopted outside of clinical settings due to the lack of a centralized public database of MS protein signatures that would facilitate isolate identification via spectral comparison. Further, current platforms lack meaningful ways to compare multiple properties from large numbers of bacterial isolates. Herein we present the IDBac web platform, a crowd-sourced central knowledgebase of protein MS signatures of >1400 strains spanning 6 bacterial phyla. Accompanying the knowledgebase is analysis infrastructure to identify unknown isolates, probe relationships within culture collections using metadata integration, and visualize specialized metabolite differences within groups of closely related bacteria. To highlight this utility and encourage wide community contribution, examples of each are presented.

  PublisherOA PDFDOI

• Table S3 from Dietary Fiber Lacks a Consistent Effect on Immune Checkpoint Blockade Efficacy Across Diverse Murine Tumor Models

  2025-09-25

  articleOpen access

  <p>Gut microbiome taxonomic classification data</p>

  PublisherDOI

• Table S12 from Dietary Fiber Lacks a Consistent Effect on Immune Checkpoint Blockade Efficacy Across Diverse Murine Tumor Models

  2025-09-25

  articleOpen access

  <p>Tumor immune profiling in the PyMT model by flow cytometry</p>

  PublisherDOI

Recent grants

• Project 4: Using Synthetic Immunology to Improve Activity and Specificity, and Overcome Resistance, in Cellular Therapy

  NIH · $138.0M · 1997–2025

• NIH Grant T32AI055409

  NIH · $1.1M · 2010

• Systems Biology of Microbiome-mediated Resilience to Antibiotic-resistant Pathogens

  NIH · $7.1M · 2016–2021

• Innate Immune Responses to Microbial Flora

  NIH · $7.7M · 1998–2020

• NIH Grant R37AI039031

  NIH · $4.5M · 2018

Frequent coauthors

• Ying Taur

  Memorial Sloan Kettering Cancer Center

  200 shared

• Marcel R.M. van den Brink

  Cornell University

  190 shared

• Ingrid M. Leiner

  140 shared

• Jonathan U. Peled

  130 shared

• Eric R. Littmann

  86 shared

• Robert R. Jenq

  84 shared

• Miguel-Ángel Perales

  80 shared

• Sergio Giralt

  Memorial Sloan Kettering Cancer Center

  72 shared

Labs

• Pamer LabPI

Education

• B.A., Biology

  Case Western Reserve University

  1977

• M.D., Medicine

  Case Western School of Medicine

  1982

• M.D., Medicine/Infectious Diseases

  University of California, San Diego

  1990