Metagenomics - Other Projects

Project Principal Investigator
Genomic Tools for Studying the Ecology of the Human Vaginal Microflora Jacques Ravel Ph.D.
Microbiome of the anterior nares Emmanuel Mongodin Ph.D.
Mucosal Immunity, Vaccines and Microbiota Interplay in Humans and Animal Models Marcelo Sztein, M.D.
Application of Genomic Advances to Wound Repair Emmanuel Mongodin Ph.D.
The role of the gut microbiota on the onset of Celiac Disease in children Jacques Ravel Ph.D., Alessio Fassano, M.D.
The effect of probiotic use in neonates on the gut microbiota and permeability Jacques Ravel Ph.D., Alessio Fassano, M.D., Rose Viscardi, M.D.
Duration of Hormonal Contraceptive Use: Immune Responses and Vaginal Microbiota Rebecca Brotman Ph.D., M.P.H., Jacques Ravel Ph.D., Khalil Ghamen, M.D.

Genomic Tools for Studying the Ecology of the Human Vaginal Microflora


The normal vaginal microflora in healthy women of reproductive age plays a key role in preventing successful colonization by "undesirable" organisms including those responsible for bacterial vaginosis, yeast infections, sexually transmitted diseases and urinary tract infections. Our long-term goal is to develop an accurate understanding of the composition and ecology of the vagina microbial ecosystem in normal, healthy women as an essential prerequisite for comprehending how the normal microflora reduces the risk of acquiring these communicable diseases and for defining the factors determining disease susceptibility. The specific hypotheses are that 1. women genetic backgrounds influence the composition of the vaginal microflora, 2. while vaginal community compositions markerdly vary amongst women, the functional potential of a community is similar. Tools necessary to test these hypotheses will be developed and are addressed by these specific aims:

1. Conduct a comprehensive survey the vaginal microflora in 400 women of different ethnic background using 16S rRNA gene sequencing analysis. We will correlate the community composition with genetic backgrounds, and provide the basis for Aim 2.

2. Develop a 16S rDNA-based molecular tool (molecular inversion probes) to rapidly and quantitatively measure the microbial species composition and abundance of a vaginal community.

3. Characterized the metabolic potential of the vaginal microflora of healthy women by community genomics. We will sequence the "community genome" of the five most predominant community types. Sequence analysis will be freely accessible through the web-based Vaginal Microbiome Database.

4. Develop the Vaginal Microbiome Expression GeneChip© array, a high-density oligonucleotide microarray-based tool for functional genomic analyses of vaginal microbial community. Using this tool we will assess community gene expression over the course of two months, while monitoring reproductive hormone levels. We view this work as analogous to the human genome project, in which initial sequence information provided a platform for decades of future work focused on all aspect of human health and disease. Similarly, these tools will be critical for the study and evaluation of women's health.

Microbiome of the anterior nares


Our microbiome contains essential bacteria that carry out key metabolic reactions that are necessary for our health but are not encoded for in the human genome. Yet these same beneficial bacteria can make us vulnerable for developing healthcare associated infections (HAI or nosocomial infections).

The CDC estimates there are 1.7 million HAI in the United States each year and almost 100,000 associated deaths. The bacteria causing these infections can be endogenous (part of our existing bacterial flora at admission) or exogenous (acquired during the hospital stay). Some of the problems caused by our existing bacteria (endogenous) of the anterior nares (e.g. S. aureus), skin (e. g. coagulase-negative Staphylococci,) and posterior pharynx (e.g. Klebsiella spp.) include surgical site infections, central-line associated blood stream infections and pneumonia. For example, 80-85% of S. aureus infections in people who are S. aureus colonized are due to the patient's endogenous isolate. The human microbiome of patients is the source of the majority of healthcare associated infections, coming from either endogenous or exogenous sources. The public reporting of HAI has fueled new initiatives to prevent healthcare associated infections. One such healthcare policy initiative is "decolonization", which is applying targeted or non-targeted antimicrobials to the skin and mucosal surfaces. Given the role of our normal flora as a barrier to infection, decolonization regimens could have unintended negative consequences.

IGS scientists are working with Dr. Mary-Claire Roghmann (U. of Maryland School of Medicine) to better understand the microbiome of the anterior nares and upper airways in populations with and without current exposure to the healthcare environment. These comparisons will give us a better understanding of the changes associated with decolonization regimens within individuals in both populations. The long term goal of this research is to use the information gained to develop new ways for better management of the human microbiome during hospital visits. Scientists and medical researchers would like to reduce the risk of healthcare associated infections without the negative consequences that can occur with strategies like decolonization.

Mucosal Immunity, Vaccines and Microbiota Interplay in Humans and
Animal Models


The introduction of vaccines over the last century has dramatically decreased morbidity and mortality from many infectious diseases. In spite of the need to develop new or improved vaccines against several enteric pathogens, their development has been impeded due to the incomplete understanding of the biological and immunological mechanisms in the complex environment of the human body. This is particularly true with regard to pathogens that enter the host via mucosal surfaces, including the gastrointestinal (GI) tract. This project is focused on furthering our understanding of the protective immunological mechanisms that can be elicited in the GI microenvironment. Moreover, because the microbiota is certain to significantly influence the access of antigens and subsequent host immune response, we propose to conduct pioneering studies on the interactions between the local intestinal microbiota and the host immune response.

Investigators at IGS are involved in four components of this project:

1) Protective immune mechanisms to Shigella dysenteriae 1 vaccines in macaques and humans.

This project will examine the impact and effectiveness of oral immunization with a S. dysenteriae 1 vaccine in human and cynomolgus macaques. We will perform an in depth analysis to identify the systemic and mucosal immunological mechanisms of protection. Additionally we will examine the impact of the vaccination and subsequent immunological response on the host microbiota.

2) Local and systemic specific immunity, microbiome and H. pylori infection in children, adults and the elderly.

This project is directed to address the overall hypothesis that the gastric mucosa harbors resident populations of non-Helicobacter bacteria that vary among individuals serve as important cofactors in determining the gastric health of the host.

3) Effect of oral immunization with the Ty21a typhoid vaccine on local and systemic immune responses and the gut microbiota in children, adults and the elderly.

This study will explore whether oral immunization with the licensed Ty21a typhoid vaccine results in perturbations of the microbiota measured in terminal ileum biopsies and stools, as well as to evaluate in depth the systemic and local immune responses elicited following immunization.

4) A novel ORFeome approach to identify CD8+ T cell responses to S. Typhi proteins in humans.

This project is directed towards the development of novel technology to identify antigens recognized by pathogen-specific class-I MHC restricted T cells by systematic screening of pathogen protein coding regions in humans.

The overreaching goal of this project is to provide critical insight into the complex interactions of the host immune systems and the microbiota.