D. Scott Merrell, Ph.D.

D. Scott Merrell, Ph.D.

D. Scott Merrell

Name: D. Scott Merrell, Ph.D.

Department of Primary Appointment: Microbiology & Immunology
Position: USU Faculty
Title: Professor

Affiliated Departments: Molecular & Cell Biology, Emerging Infectious Diseases

Research Interests:
Host-pathogen interactions

Email: douglas.merrell@usuhs.edu (link sends e-mail)
Office Phone: (301) 295-1584
Lab Phone: (301) 319-8022
Fax Number: (301) 295-3773
Room: B4140

Department Website
PubMed Listing


Ph.D., Tufts University School of Medicine



  • 1988-1992 - B.S. Biology magna cum laude, 1992, Lyon College, Batesville, Arkansas
  • 1994-1996 M.S. Microbiology, 1996, University of Arkansas, Fayetteville, Arkansas, Advisor: Mack Ivey
  • 1996-2001 Ph.D. Molecular Biology and Microbiology, 2001, Tufts University School of Medicine, Boston, Massachusetts, Advisor: Andrew Camilli
  • 2001-2004 Postdoctoral Fellow, Stanford School of Medicine, Advisor: Stanley Falkow


Research in the Merrell lab focuses on 4 main areas:

  1. Fur-regulation and iron-dependent gene expression.
  2.  H. pylori therapeutics.
  3. Virulence factor polymorphisms and epidemiology.
  4. Metagenomics of infectious disease.

Fur-regulation and Iron-dependent Gene Expression

Iron is a critical nutrient for the vast majority of living organisms on the planet and bacteria are no exception. However, there is a fine line between too little and too much iron. One way that iron homeostasis is maintained in bacteria is through the use of the Ferric Uptake Regulator (Fur). Fur typically functions by repressing genes whose functions are usually related to iron uptake and storage. This occurs under conditions of iron abundance when the protein is bound by its ferrous iron cofactor. While this is by far the most common type of Fur regulation, iron-bound Fur has also been shown to function as an activator of some genes. In Helicobacter pylori, Fur has the ability to repress and activate genes in its iron-bound form, as well as in its apo form (i.e. in the absence of its ferrous iron cofactor). apo-Fur regulation has not been definitively shown to occur in any other bacterial species, making the study of Fur regulation of particular interest in H. pylori. Additionally, it is clear from transcriptional analyses that Fur controls expression of genes with a broad array of functions. In H. pylori, it has been demonstrated that Fur regulates genes involved in iron uptake and storage, genes that mediate oxidative, pH, and osmotic stress, genes involved in metabolism, and even genes that encode virulence factors. Numerous animal studies have also shown that Fur play a clear role in pathogenesis as animals infected with fur mutant strains show less pathology and slower disease progression than their wild-type infected counter parts. It is clear that Fur is crucial to the overall success of H. pylori as a pathogen.

 H. pylori Fur regulation is currently being explored in the lab from many different perspectives. First we are interested in understanding the structure - function relationships that allow for both iron-bound and apo-Fur regulation. These studies involve the characterization of both site specific fur mutants as well as a mutant library carrying random mutations in the fur coding region. In addition, we are interested in dissecting the role of iron-bound versus apo-Fur regulation in pathogenesis and stress adaptation. As there is not a well-defined DNA binding sequence for H. pylori Fur, ongoing studies seek to better define these binding regions, which are called "Fur boxes". Other areas of interest include expanding the known iron-bound and apo-Fur regulons. Going hand in hand with the Fur related work, other projects in the lab are geared towards further exploring and defining the iron-uptake systems utilized by H. pylori.

The goal of these projects is to better understand the contributions of Fur and iron regulation in H. pylori pathogenesis as well as to broaden our understanding of the role Fur plays in bacterial survival.

 H. pylori Therapeutics

There are three broad categories of potential treatment strategies for eradication of Helicobacter pylori infection: vaccination, antimicrobials, and naturopathic therapies. Currently there are no licensed vaccines or approved naturopathic therapies for H. pylori, so antibiotics have been used for treatment of the infection. However, the chronic nature of H. pylori colonization and eradication difficulties are responsible for the evolution of H. pylori antibiotic treatment strategies from mono to dual to triple therapies, and more recently to quadruple, sequential and rescue therapies. Metronidazole (MTZ), clarithromycin (CLR), tetracycline (TET) and amoxicillin (AMX) are the three antibiotics most currently used for treatment, which typically involve a combination of two or three antibiotics and a proton pump inhibitor. However, H. pylori is increasingly resistant to MTZ and CLR, and to a lesser extent to AMX. As a result, there has been an increasing rate of treatment failure, a need for more combinations of antibiotics, an increasing length of treatment period and an overall increased cost of therapy.

Although H. pylori is generally viewed as an extracellular pathogen, a growing body of evidence has established that a subset of the infecting H. pylori population becomes intracellular. It is evident that conventional antibiotics used to treat H. pylori infection likely do not reach suitable concentrations inside the host cell to sterilize the environment. Thus, there is an emerging belief that the ability of H. pylori to survive inside host cells may be partially responsible for treatment failure, and in turn, the spread of drug-resistant strains. To this end, our laboratory is involved in the development and study of novel antibiotics with the ability to traverse the host cell membrane and kill intracellular bacteria.

Virulence Factor Polymorphisms and Epidemiology

As a species, H. pylori is known to show an amazing level of genetic variability across strains. This diversity includes changes in overall gene content as well as polymorphism in gene products. Included among the list of genes that show variation are many that encode virulence factors. Numerous studies suggest that polymorphism in some of these factors may be partially responsible for the wide variety of possible disease outcomes that result from H. pylori infection; certain polymorphic forms of particular factors may be more virulent and cause more disease. We are investigating this possibility by conducting molecular epidemiological studies that attempt to correlate virulence factor genotype with clinical outcome of infection. Furthermore, we are conducting molecular studies that are focused specifically on the CagA toxin. CagA is a type IV secreted effector protein that is injected directly into host cells and causes dramatic alterations in host cell signaling. Studies in transgenic animals have shown that CagA is an oncoprotein; expression of CagA is sufficient to cause cancer in the transgenic animals. Based on the importance of the toxin in cancer development and our epidemiologic data that indicate that particular variants of the toxin are more toxic, we are currently utilizing isogenic H. pylori strains that differ only in the form of the toxin that they express to determine how toxin variation differentially affects various host signaling pathways.

Metagenomics of Infectious Disease

It is estimated that the bacterial cells found in and on the human body actually outnumber the human cells 100 to 1. These bacteria, which are known as our normal microflora, serve as the "first line of defense" against microbial pathogens, and are necessary for many essential processes. Recent advances in sequencing technology have begun to allow researchers to define members of the normal human microflora in both healthy and diseased states. As a result, it has become increasingly clear that the composition of the microbial community plays a significant role in maintaining the delicate balance between health and disease states.

Using 16S rRNA amplicon based studies, we are currently involved in collaborative efforts to 1) analyze bacterial population structures and 2) determine whether differences within these populations are associated with the pathogenesis of human disease. By defining the community members found in both healthy and diseased states, we hope to advance our current knowledge of how the presence or absence of particular community members protects, or fails to protect, against infection. In addition, identification of "keystone" members of the community may provide therapeutic or probiotic targets for disease treatment.

Examples of ongoing projects include analysis of microbial communities associated with tumor growth, as well as poly-microbial and multi-drug resistant bacterial infections.