Marwa ElRakaiby
Bas E. Dutilh
Mariam R. Rizkallah
Annemarie Boleij
Jason N. Cole
Ramy K. Aziz

A summary of key findings and applications from the Human Microbiome Project.


The Human Microbiome Project (HMP) is a global initiative undertaken to identify and characterize the collection of human-associated microorganisms at multiple anatomic sites (skin, mouth, nose, colon, vagina), and to determine how intra-individual and inter-individual alterations in the microbiome influence human health, immunity, and different disease states. In this review article, we summarize the key findings and applications of the HMP that may impact pharmacology and personalized therapeutics. We propose a microbiome cloud model, reflecting the temporal and spatial uncertainty of defining an individual's microbiome composition, with examples of how intra-individual variations (such as age and mode of delivery) shape the microbiome structure. Additionally, we discuss how this microbiome cloud concept explains the difficulty to define a core human microbiome and to classify individuals according to their biome types. Detailed examples are presented on microbiome changes related to colorectal cancer, antibiotic administration, and pharmacomicrobiomics, or drug–microbiome interactions, highlighting how an improved understanding of the human microbiome, and alterations thereof, may lead to the development of novel therapeutic agents, the modification of antibiotic policies and implementation, and improved health outcomes. Finally, the prospects of a collaborative computational microbiome research initiative in Africa are discussed.

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Marwa ElRakaiby and Ramy K. Aziz ([email protected]) are affiliated with the Department of Microbiology and Immunology, Faculty of Pharmacy at Cairo University, Egypt. Bas E. Dutilh is affiliated with the Centre for Molecular and Biomolecular Informatics, Radbound Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands; and the Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, UFRJ, Rio de Janeiro. Mariam R. Rizkallah is affiliated with the American University in Cairo, Egypt. Annemarie Boleij is affiliated with the Department of Medicine, Division of Infectious Diseases, Johns Hopkins University-School of Medicine in Baltimore, Maryland. Jason N. Cole is affiliated with the School of Chemistry and Molecular Biosciences, and the Australian Infectious Diseases Research Centre of the University of Queensland in Australia; and also with the Department of Pediatrics at UCLA.

OMICS: A Journal of Integrative Biology, published by Mary Ann Liebert, Inc., integrates global high-throughput and systems approaches to 21st century science from “cell to society”—seen from a post-genomics perspective. The above article was first published in OMICS online ahead of print in May of 2014 with the title “Pharmacomicrobiomics: The Impact of Human Microbiome Variations on Systems Pharmacology and Personalized Therapeutics”. The views expressed here are those of the authors and are not necessarily those of OMICS journal, Mary Ann Liebert, Inc., publishers, or their affiliates. No endorsement of any entity or technology is implied.

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