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
IDBac: an open-access web platform to identify bacteria and analyze relationships in culture collections using MALDI-TOF mass spectrometry.
IDBac: an open-access web platform to identify bacteria and analyze relationships in culture collections using MALDI-TOF mass spectrometry. Nat Commun. 2026 Jul 23; 17(1).
PMID: 42637730
Host metabolism can produce many indoles and phenols independently of the microbiome.
Host metabolism can produce many indoles and phenols independently of the microbiome. Nat Metab. 2026 Jul; 8(7):1528-1544.
PMID: 42337138
Microbiome histidine competition mediates dietary control of systemic imidazole propionate.
Microbiome histidine competition mediates dietary control of systemic imidazole propionate. bioRxiv. 2026 Jun 23.
PMID: 42395374
Intracellular acidification by microbiota-derived valeric acid facilitates trans-kingdom ecology limiting Candida parapsilosis colonization.
Intracellular acidification by microbiota-derived valeric acid facilitates trans-kingdom ecology limiting Candida parapsilosis colonization. Cell Host Microbe. 2026 Jul 08; 34(7):1320-1332.e6.
PMID: 42242207
Fecal butyrate and deoxycholic acid quantitation for rapid assessment of the gut microbiome.
Fecal butyrate and deoxycholic acid quantitation for rapid assessment of the gut microbiome. PLoS One. 2026; 21(1):e0337727.
PMID: 41511994
Lantibiotic-producing bacteria impact microbiome resilience and colonization resistance.
Lantibiotic-producing bacteria impact microbiome resilience and colonization resistance. Cell Host Microbe. 2025 12 10; 33(12):2100-2114.e6.
PMID: 41330369
IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry.
IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry. bioRxiv. 2025 Oct 15.
PMID: 41279347
Dietary Fiber Lacks a Consistent Effect on Immune Checkpoint Blockade Efficacy Across Diverse Murine Tumor Models.
Dietary Fiber Lacks a Consistent Effect on Immune Checkpoint Blockade Efficacy Across Diverse Murine Tumor Models. Cancer Res. 2025 09 02; 85(17):3335-3347.
PMID: 40540354
Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples.
Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples. Nat Biotechnol. 2026 May; 44(5):752-758.
PMID: 40629040
Flagellar switch inverted repeats impact heterogeneity in flagellar gene expression and thus C. difficile RT027/MLST1 virulence.
Flagellar switch inverted repeats impact heterogeneity in flagellar gene expression and thus C. difficile RT027/MLST1 virulence. Cell Rep. 2025 Jun 24; 44(6):115830.
PMID: 40504685