The Human Microbiome Project was conceived almost 15 years ago, as an extension of the Human Genome Project, to explore the diversity of human-associated microorganisms at multiple body sites (skin, mouth, nose, colon, and vagina) and their impact on human health.  Pioneering studies highlighted the extent of intra- and inter-individual microbiome variations, and how these variations played key roles in nutrition, health, disease, and immunity. Different models were proposed to describe the human microbiome, likening it, for example, to a missing organ or a second genome. The origin and definition of the term microbiome is discussed, and different views of illustrating or modeling the microbiome are debated, including a proposed cloud model. Subsequently, the major obstacles/bottlenecks related to microbiome analysis are listed, and examples of analysis strategies that address them are presented. Moreover, recent research results are presented on microbiome alterations in hepatitis C and conjunctivitis patients, as well as the interplay between the human and surrounding environmental microbes among nurses and drug factory workers. Finally, the nascent field of pharmacomicrobiomics, or drug–microbiome interactions, is introduced and discussed in the light of ‘the microbiome cloud model’. Key examples of drugs that are dramatically affected by gut and vaginal microbes are presented. Finally, recently developed web resources and big data analysis tools are demonstrated and applied to accelerate drug-microbiome interactions in the hope of customizing therapeutic intervention, minimizing drug toxicity, and improving the therapeutic outcomes of available medicines.

Learning Objectives:

1. List and compare the different definitions of, and images associated with, the terms microbiome and human microbiome.

2. Define pharmacomicrobiomics, and differentiate the term from the associated subfields of pharmacometagenomics, pharmacometabonomics, pharmacometabonomics

3. List the major bottleneck in the microbiome analysis pipeline, and mention at least one strategy to address each of them

4. List potential applications of pharmacomicrobiomics in precision medicine (therapeutics and diagnostics).