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
Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom.
Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom. Cell Syst. 2025 Feb 19; 16(2):101167.
PMID: 39826551
Protection against Clostridioides difficile disease by a naturally avirulent strain.
Protection against Clostridioides difficile disease by a naturally avirulent strain. Cell Host Microbe. 2025 Jan 08; 33(1):59-70.e4.
PMID: 39610252
Flagellar switch inverted repeat impacts flagellar invertibility and varies Clostridioides difficile RT027/MLST1 virulence.
Flagellar switch inverted repeat impacts flagellar invertibility and varies Clostridioides difficile RT027/MLST1 virulence. bioRxiv. 2024 Sep 24.
PMID: 39386689
Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution.
Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution. Cell Host Microbe. 2024 Oct 09; 32(10):1853-1867.e5.
PMID: 39293438
Gut microbes fend off harmful bacteria by depriving them of nutrients.
Gut microbes fend off harmful bacteria by depriving them of nutrients. Nature. 2024 Sep; 633(8031):774-775.
PMID: 39294279
Protection against Clostridioides difficile disease by a naturally avirulent C. difficile strain.
Protection against Clostridioides difficile disease by a naturally avirulent C. difficile strain. bioRxiv. 2024 May 07.
PMID: 38766138
Intestinal carbapenem-resistant Klebsiella pneumoniae undergoes complex transcriptional reprogramming following immune activation.
Intestinal carbapenem-resistant Klebsiella pneumoniae undergoes complex transcriptional reprogramming following immune activation. Gut Microbes. 2024 Jan-Dec; 16(1):2340486.
PMID: 38659243
Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution.
Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution. bioRxiv. 2024 Mar 09.
PMID: 38496653
Activity of Gut-Derived Nisin-like Lantibiotics against Human Gut Pathogens and Commensals.
Activity of Gut-Derived Nisin-like Lantibiotics against Human Gut Pathogens and Commensals. ACS Chem Biol. 2024 02 16; 19(2):357-369.
PMID: 38293740
Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration.
Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration. Nat Microbiol. 2024 Jan; 9(1):55-69.
PMID: 38177297