Advanced Metagenomic Analysis of Human Gastrointestinal Microbiota in Patients With Chronic GI Disorders (IBS, IBD, CRC)
The terms intestinal "microflora" or "microbiota" refer to the microbial ecosystem
colonizing the gastrointestinal tract. Recently developed molecular biology instruments
suggest that a substantial part of bacterial communities within the human gut still have to
be described. Intestinal bacteria play an essential role in the development and homeostasis
of the immune system. Most of these important microbiota are unculturable which
significantly have limited our understanding of bacterial-host crosstalk. Among the methods
designed to gain access to the physiology and genetics of uncultured organisms,
metagenomics, the genomic analysis of a population of microorganisms, has emerged as a
powerful technology. Metagenomics is the study of genomic content in a complex mixture of
microorganisms. Direct isolation of genomic DNA from an environment circumvents culturing
the organisms under study. The two primary goals of this approach are to develop a consensus
of what populations of microorganisms are presents and then to identify what roles each
microorganism has within a specific environment. Metagenomics samples are found nearly
everywhere, including several microenvironments within the human gut, soil samples, extreme
environments such as deep mines and the various layers within the ocean. Therefore, the
diversity of microorganisms is thought to be in the range of hundreds of millions to greater
than tens of trillions of species. Among the most mysterious microenvironment is the human
gastrointestinal tract that harbor greater than thousands of millions of microbial species
(at least 1014), including up to 2000 species dominated by anaerobic bacteria.
Many of the gastrointestinal or even other diseases (metabolic as in obesity, or autoimmune
as in allergies) involve primarily the human gut microbiota and then according to specific
changes in microbiota equilibrium certain effects occur on either bowel motility (as in
irritable bowel syndrome: IBS), homeostasis of the GI immune system (as in inflammatory
bowel disease: IBD), or mucosal cells proliferation (as in adenoma - colorectal cancer:
CRC). These chronic diseases affect all nations worldwide and represent a significant public
health burden. They can be seen among children, adolescents, and adults. Currently there is
no medical cure for IBS, IBD or CRC once they develop.
The complex interactions between microbial, genetic, immune, and environmental factors seem
to play an important role in the pathogenesis of IBS, IBD and CRC. Lately, post infectious -
IBS have gained increasing focus, to the extent that whole pathogenesis of IBS might be
attributed to a specific triggering factor of microbiota balance. The prevailing theory is
that IBD is related to an altered mucosal barrier with a deregulated immune response
directed against specific modifications in the normal microbiota leading to the alteration
of its equilibrium. The etiology of IBD can therefore be conceptualized as an aberrant
immunologic response to a modified component or components of the gut microbiota potentially
following an environmental insult. Likewise, CRC development process from normal mucosal
surface to adenoma and finally to CRC; is probably related to gut microbiota.
The prevalence of these diseases has been documented to go through an obvious increase in
Saudi Arabia during the last 2 decades. This would represent a unique model to study the
role of GIT microbiota or their metagenomics and their modifications in response to
environmental or dietary factors in this community that went into urbanization fairly
recently, and then analyze their causative relations to the focus diseases.
Here, we propose to perform a comprehensive analysis of the gastrointestinal tract
microbiota and its contribution on gut homeostasis in normal subjects and patients with IBS,
IBD and CRC by using state of the art metagenomics technology. This will be done on a Saudi
population sample that we believe represent a unique model.
Our specific objectives for this project are:
- Characterize the microbiota composition (microbes and virus) of the mucosa from Saudi
patients with IBS, IBD and CRC.
- Characterize the mobile GI metagenomics of Saudi patients with IBS, IBD and CRC.
- Compare the metagenomics of IBS, IBD and CRC patients to each other and to normal
subjects from the same population.
Expected outcomes and Significance of research:
Altogether, the results from aims 1 and 2 will provide for the first time a comprehensive
and in-depth analysis of the mucosa-associated microbiota of adult patients with IBS, IBD
and CRC in Saudi population. The proposed study will define a microbiota "fingerprint" for
Saudi norms, IBS, IBD and CRC. The contribution of virome and the mobile metagenome into
these diseases development and/or health maintenance will be assessed for the first time and
thus has the potential to reveal new paradigms. In addition, the study of the virome and
mobile metagenome will help us to understand the selective forces that could contribute to
the alteration and evolution of the microbiota community and thus could have important
implications for the treatment of the diseases. Certainly, the work proposed here will pave
the way toward future hypothesis-driven research which could lead to the design of
therapeutic strategies aimed at manipulating the microbial community.
Observational Model: Case Control, Time Perspective: Cross-Sectional
mucosa associated microbiota pattern
collection of samples as per protocol and characterizing the pattern numerically in each subject of the study groups and compare them to controls
Ahmed O AlOmair, MD
Saudi Arabia: King AbdulAziz City for Science and Technology