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, 18 (7), 402-14

Pharmacomicrobiomics: The Impact of Human Microbiome Variations on Systems Pharmacology and Personalized Therapeutics


Pharmacomicrobiomics: The Impact of Human Microbiome Variations on Systems Pharmacology and Personalized Therapeutics

Marwa ElRakaiby et al. OMICS.


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.


<b>FIG. 1.</b>
FIG. 1.
An illustration of the human supraorganism represented as a human body surrounded by a “microbiome cloud” at two health states, using Leonardo da Vinci's classic “Vitruvian Man.” From a genomic perspective, a human can be viewed as a relatively stable gene pool surrounded by a fluid microbial cloud or aura made up of a highly diverse set of microbes. In spite of evidence of memory that preserves the composition of an individual's microbiome, one's microbiome still varies continually with time, space, health state, and other intra-individual factors. Here, two different microbiome patterns are shown on the right and left of the same individual, representing variation in types and abundance of microbial species.
<b>FIG. 2.</b>
FIG. 2.
A model for bacterial involvement in a progressing colorectal cancer (CRC) tumor. Several important driver and passenger bacteria associated with the different tumor stages are shown. For details and associated references, see text.
<b>FIG. 3.</b>
FIG. 3.
Monthly visitor analysis of the PharmacoMicrobiomics web portal between November 2011 and December 2013. Data obtained from StatCounter and publicly available at the URL:
<b>FIG. 4.</b>
FIG. 4.
Increase in number of citations and usage of the term “pharmacomicrobiomics” in the past 3 years based on data generated by Google Scholar (URL:, accessed 20 Jan 2014) and the records in PharmacoMicrobiomics database from 2011–2013.

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