Our Faculty

Eric Gerd Pamer, MD

Humans and other mammals are colonized by complex populations of microbes that constitute the microbiota. Some commensal bacteria enhance immune defenses by inducing host expression of antimicrobial factors while others secrete antimicrobial molecules that inhibit pathogens. We study interactions between pathogenic and beneficial bacteria and their mammalian hosts. Our laboratory’s research focuses on a wide range of commensal bacteria that have been characterized at the genomic, proteomic and metabolomic level and we are using gnotobiotic mice to test assembled commensal consortia for their ability to enhance resistance against pathogenic bacteria. Using these platforms, we have identified multiple novel mechanisms of antimicrobial resistance that can be exploited to reduce the risk of infection by highly antibiotic-resistant pathogens.



Our laboratory has worked closely with clinical groups to investigate the role of the microbiota in clinical outcomes. We have demonstrated that loss of microbiota diversity during allogeneic hematopoietic cell transplantation adversely impacts outcomes and have investigated the impact of microbiota composition on the risk of developing colitis during checkpoint blockade cancer immunotherapy.

University of California, San Diego
San Diego, California
- Medicine/Infectious Diseases
1990

Case Western School of Medicine
Cleveland, Ohio
MD - Medicine
1982

Case Western Reserve University
Cleveland, Ohio
BA - Biology
1977

Translating Microbiome Research From and To the Clinic.
Zhang ZJ, Lehmann CJ, Cole CG, Pamer EG. Translating Microbiome Research From and To the Clinic. Annu Rev Microbiol. 2022 09 08; 76:435-460.
PMID: 35655344

A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients.
Yan J, Liao C, Taylor BP, Fontana E, Amoretti LA, Wright RJ, Littmann ER, Dai A, Waters N, Peled JU, Taur Y, Perales MA, Siranosian BA, Bhatt AS, van den Brink MRM, Pamer EG, Schluter J, Xavier JB. A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients. Sci Data. 2022 05 18; 9(1):219.
PMID: 35585088

Gut microbiome correlates of response and toxicity following anti-CD19 CAR T cell therapy.
Smith M, Dai A, Ghilardi G, Amelsberg KV, Devlin SM, Pajarillo R, Slingerland JB, Beghi S, Herrera PS, Giardina P, Clurman A, Dwomoh E, Armijo G, Gomes ALC, Littmann ER, Schluter J, Fontana E, Taur Y, Park JH, Palomba ML, Halton E, Ruiz J, Jain T, Pennisi M, Afuye AO, Perales MA, Freyer CW, Garfall A, Gier S, Nasta S, Landsburg D, Gerson J, Svoboda J, Cross J, Chong EA, Giralt S, Gill SI, Riviere I, Porter DL, Schuster SJ, Sadelain M, Frey N, Brentjens RJ, June CH, Pamer EG, Peled JU, Facciabene A, van den Brink MRM, Ruella M. Gut microbiome correlates of response and toxicity following anti-CD19 CAR T cell therapy. Nat Med. 2022 04; 28(4):713-723.
PMID: 35288695

Microbiome-based therapeutics.
Sorbara MT, Pamer EG. Microbiome-based therapeutics. Nat Rev Microbiol. 2022 06; 20(6):365-380.
PMID: 34992261

Compositional Flux Within the Intestinal Microbiota and Risk for Bloodstream Infection With Gram-negative Bacteria.
Stoma I, Littmann ER, Peled JU, Giralt S, van den Brink MRM, Pamer EG, Taur Y. Compositional Flux Within the Intestinal Microbiota and Risk for Bloodstream Infection With Gram-negative Bacteria. Clin Infect Dis. 2021 12 06; 73(11):e4627-e4635.
PMID: 31976518

A multisite genomic epidemiology study of Clostridioides difficile infections in the USA supports differential roles of healthcare versus community spread for two common strains.
Miles-Jay A, Young VB, Pamer EG, Savidge TC, Kamboj M, Garey KW, Snitkin ES. A multisite genomic epidemiology study of Clostridioides difficile infections in the USA supports differential roles of healthcare versus community spread for two common strains. Microb Genom. 2021 06; 7(6).
PMID: 34180789

Author Correction: Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients.
Liao C, Taylor BP, Ceccarani C, Fontana E, Amoretti LA, Wright RJ, Gomes ALC, Peled JU, Taur Y, Perales MA, van den Brink MRM, Littmann E, Pamer EG, Schluter J, Xavier JB. Author Correction: Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients. Sci Data. 2021 Apr 23; 8(1):119.
PMID: 33893321

Fecal microbiota diversity disruption and clinical outcomes after auto-HCT: a multicenter observational study.
Khan N, Lindner S, Gomes ALC, Devlin SM, Shah GL, Sung AD, Sauter CS, Landau HJ, Dahi PB, Perales MA, Chung DJ, Lesokhin AM, Dai A, Clurman A, Slingerland JB, Slingerland AE, Brereton DG, Giardina PA, Maloy M, Armijo GK, Rondon-Clavo C, Fontana E, Bohannon L, Ramalingam S, Bush AT, Lew MV, Messina JA, Littmann E, Taur Y, Jenq RR, Chao NJ, Giralt S, Markey KA, Pamer EG, van den Brink MRM, Peled JU. Fecal microbiota diversity disruption and clinical outcomes after auto-HCT: a multicenter observational study. Blood. 2021 03 18; 137(11):1527-1537.
PMID: 33512409

Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients.
Liao C, Taylor BP, Ceccarani C, Fontana E, Amoretti LA, Wright RJ, Gomes ALC, Peled JU, Taur Y, Perales MA, van den Brink MRM, Littmann E, Pamer EG, Schluter J, Xavier JB. Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients. Sci Data. 2021 03 02; 8(1):71.
PMID: 33654104

TAM mediates adaptation of carbapenem-resistant Klebsiella pneumoniae to antimicrobial stress during host colonization and infection.
Jung HJ, Sorbara MT, Pamer EG. TAM mediates adaptation of carbapenem-resistant Klebsiella pneumoniae to antimicrobial stress during host colonization and infection. PLoS Pathog. 2021 02; 17(2):e1009309.
PMID: 33556154

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