Pamer Lab

Welcome to the Eric Pamer Laboratory

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.  The Eric Pamer laboratory studies 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.

Recent Original Publications

Becattini S, Littmann ER, Seok R, Amoretti L, Fontana E, Wright R, Gjonbalaj M, Leiner IM, Plitas G, Hohl TM, Pamer EG. Enhancing mucosal immunity by transient microbiota depletion. Nat Commun. 2020 Sep 8;11(1):4475. doi: 10.1038/s41467-020-18248-4. 

Sorbara MT, Littmann ER, Fontana E, Moody TU, Kohout CE, Gjonbalaj M, Eaton V, Seok R, Leiner IM, Pamer EG. Functional and Genomic Variation between Human-Derived Isolates of Lachnospiraceae Reveals Inter- and Intra-Species Diversity. Cell Host Microbe. 2020 Jul 8;28(1):134-146.e4. doi: 10.1016/j.chom.2020.05.005. 

Gjonbalaj M, Keith JW, Do MH, Hohl TM, Pamer EG, Becattini S.  Antibiotic Degradation by Commensal Microbes Shields Pathogens. Infect Immun. 2020 Mar 23;88(4):e00012-20. doi: 10.1128/IAI.00012-20.

Keith JW, Dong Q, Sorbara MT, Becattini S, Sia JK, Gjonbalaj M, Seok R, Leiner IM, Littmann ER, Pamer EG. Impact of Antibiotic-Resistant Bacteria on Immune Activation and Clostridioides difficile Infection in the Mouse Intestine.  Immun. 2020 Mar 23;88(4):e00362-19. doi: 10.1128/IAI.00362-19. Print 2020 Mar 23.

Peled JU, Gomes ALC, Devlin SM, Littmann ER, Taur Y, Sung AD, Weber D, Hashimoto D, Slingerland AE, Slingerland JB, Maloy M, Clurman AG, Stein-Thoeringer CK, Markey KA, Docampo MD, Burgos da Silva M, Khan N, Gessner A, Messina JA, Romero K, Lew MV, Bush A, Bohannon L, Brereton DG, Fontana E, Amoretti LA, Wright RJ, Armijo GK, Shono Y, Sanchez-Escamilla M, Castillo Flores N, Alarcon Tomas A, Lin RJ, Yáñez San Segundo L, Shah GL, Cho C, Scordo M, Politikos I, Hayasaka K, Hasegawa Y, Gyurkocza B, Ponce DM, Barker JN, Perales MA, Giralt SA, Jenq RR, Teshima T, Chao NJ, Holler E, Xavier JB, Pamer EG, van den Brink MRM. Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation. N Engl J Med. 2020 Feb 27;382(9):822-834. doi: 10.1056/NEJMoa1900623.

Stoma I, Littmann ER, Peled JU, Giralt S, van den Brink MRM, Pamer EG, Taur Y.Clin Compositional flux within the intestinal microbiota and risk for bloodstream infection with gram-negative bacteria. Infect Dis. 2020 Jan 24:ciaa068. doi: 10.1093/cid/ciaa068. 

Kim SG, Becattini S, Moody TM, Shliaha PV, Littmann ER, Seok R, Gjonbalaj M, Eaton V, Fontana E, Amoretti L, Wright R, Caballero S, Wang Z-MX, Jung H-J, Morjaria SM, Leiner IM, Qin W, Ramos RJJF, Cross JR, Narushima S, Hon da K, Peled JU, Hendrickson RC, Taur Y, van den Brink MRM, Pamer EG. Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus.  Nature. 2019; Aug;572(7771):665-669.

Caballero S, Kim S, Carter RA, Leiner IM, Sušac B, Miller L, Kim GJ, Ling L, Pamer EG. Cooperating Commensals Restore Colonization Resistance to Vancomycin-Resistant Enterococcus faecium. Cell Host Microbe. 2017; 21(5):592-602.

Xiong H, Keith JW, Samilo DW, Carter RA, Leiner IM, Pamer EG. Innate Lymphocyte/Ly6C(hi) Monocyte Crosstalk Promotes Klebsiella pneumoniae Clearance. Cell. 2016; 165(3):679-89.

Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, No D, Liu H, Kinnebrew M, Viale A, Littmann E, van den Brink MR, Jenq RR, Taur Y, Sander C, Cross J, Toussaint NC, Xavier JB, Pamer EG. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature. 2014; 517:205-8.

Review Articles

Keith JW, Pamer EG. Enlisting commensal microbes to resist antibiotic- resistant pathogens. Journal of Experimental Medicine. 2019; 216(1):10-19.

Sorbara MT, Pamer EG. Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them. Mucosal Immunology. 2019:12(1):1-9.

Pamer EG. Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens. Science.  2016; 352(6285):535-8.

Kim S, Covington A, Pamer EG.  The Intestinal Microbiota: Antibiotics, Colonization Resistance, and Enteric Pathogens.  Immunological Reviews. 2017; 279(1):90-105.

Lewis BB, Pamer EG. Microbiota Therapy for Clostridium difficile and Antibiotic Resistant Enteric Infections. Annual Reviews of Microbiology. 2017; 71:157-178.

Pamer EG. Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens. Science.  2016; 352(6285):535-8.

Abt MC, McKenney PT, Pamer EG. Clostridium difficile colitis: pathogenesis and host defense. Nature Reviews Microbiology. 2016; 14(10):609-20.

Current Research

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