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Raphael H. Valdivia

Nanaline H. Duke Distinguished Professor of Molecular Genetics and Microbiology
Integrative Immunobiology
3110 MSRB III, Box 3580, Durham, NC 27710
3110 MSRB III Box 3580, 3 Genome Court, Durham, NC 27710

Overview


My laboratory is interested in microbes that influence human health, both in the context of host-pathogen and host-commensal interactions. For many pathogens, and certainly for most commensal microbes, we have an incomplete molecular understanding of how host and microbial factors contribute to health and disease. My research group focuses on two experimental systems:

Chlamydia trachomatis infections are responsible for the bulk of sexually transmitted bacterial diseases and are the leading cause of infectious blindness (trachoma) in the world. Chlamydia  resides within a membrane bound compartment (“inclusion”). From this location, the pathogen manipulates the cytoskeleton, inhibits lysosomal recognition of the inclusion, activates signaling pathways, re-routes lipid transport, and prevents the onset of programmed cell death. Our laboratory focuses on identifying and characterizing the bacterial factors that are secreted into the host cell cytoplasm to manipulate eukaryotic cellular functions. We use a combination of cell biology, biochemistry, genetics, genomics, proteomics and molecular biology to determining the function of virulence factors that reveal novel facets of the host-pathogen interaction. Our goal is to understand how these obligate intracellular bacterial pathogens manipulate host cellular functions to replicate, disseminate and cause disease, and in the process develop strategies to ameliorate the damage caused by these infections to the female reproductive organs.

Akkermansia muciniphila is prevalent member of the gut microbiota that proliferates in the mucus layers of our lower gastrointestinal tract and contribute to nutrient homeostasis and human immunological health. My research group developed genetic tools to characterize these microbes to define the mechanisms used to colonize the human gut and identify the molecular and cellular pathways that underscore Akkermansia's impact on immune homeostasis.  In the process, we seek to engineer strains of Akkermansia that enhance their probiotic potential.

Current Appointments & Affiliations


Nanaline H. Duke Distinguished Professor of Molecular Genetics and Microbiology · 2022 - Present Integrative Immunobiology, Basic Science Departments
Professor in Integrative Immunobiology · 2022 - Present Integrative Immunobiology, Basic Science Departments
Chair, Department of Immunology · 2022 - Present Integrative Immunobiology, Basic Science Departments
Professor of Cell Biology · 2022 - Present Cell Biology, Basic Science Departments
Professor of Molecular Genetics and Microbiology · 2023 - Present Molecular Genetics and Microbiology, Basic Science Departments
Member of the Duke Cancer Institute · 2021 - Present Duke Cancer Institute, Institutes and Centers

In the News


Published February 26, 2025
Understanding the Human Immune System
Published August 15, 2023
Scientists Unlock Secrets of Gut Bacteria Linked to Heart Health
Published September 8, 2022
Chlamydia’s Stealthy Cloaking Device Identified

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Recent Publications


The Chlamydia effector Dre1 binds dynactin to reposition host organelles during infection.

Journal Article Cell Rep · April 22, 2025 The obligate intracellular pathogen Chlamydia trachomatis replicates in a specialized membrane-bound compartment where it repositions host organelles during infection to acquire nutrients and evade host surveillance. We describe a bacterial effector, Dre1, ... Full text Link to item Cite

Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.

Journal Article bioRxiv · March 26, 2025 The human gut microbiome within the gastrointestinal tract continuously adapts to variations in diet, medications, and host physiology. A strategy for bacterial genetic adaptation is epigenetic phase variation (ePV) mediated by bacterial DNA methylation, w ... Full text Link to item Cite
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Recent Grants


Mucus-degrading intestinal bacteria and toxicities of hematopoietic cell transplantation

ResearchPrincipal Investigator · Awarded by City of Hope · 2024 - 2029

Interferon-inducible cell-intrinsic host defense against Chlamydia trachomatis

ResearchCo Investigator · Awarded by National Institute of Allergy and Infectious Diseases · 2024 - 2028

Duke Training Grant in Digestive Diseases and Nutrition

Inst. Training Prgm or CMEPreceptor · Awarded by National Institutes of Health · 1988 - 2027

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Education, Training & Certifications


Stanford University · 1998 Ph.D.