Chapter 15 : The Human Microbiome

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The total number of bacteria in the human body is at least 10 times greater than the number of human cells, and recent studies, particularly the efforts of the National Institutes of Health Human Microbiome Project consortium, have led to a greater understanding of the identity and distribution of the microorganisms that constitute these populations. In particular, implementation of next-generation sequencing (NGS) has helped illuminate how these bacteria contribute to, and are affected by, human health and disease. Significant progress in cataloging and characterizing these organisms and genes has been made in recent years thanks to NGS approaches, and studies have been expanded beyond those focused solely on the microbes that colonize the gut. The newest DNA sequencing platforms are making it possible to sequence the DNA of the collective genome (or metagenome) of entire communities of microbes from all body sites, at various stages of health and disease, over significant periods of time, effectively enabling the characterization of the “human microbiome.”

Citation: Versalovic J, Highlander S, Petrosino J. 2015. The Human Microbiome, p 226-237. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch15
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Image of FIGURE 1

Model for microbiome data generation and analyses. (A) Various components (green) and processes (lavender) involved in microbiome projects. (B) Processes of sequencing data generation/editing and data analyses (bioinformatic strategies). Adapted from with permission from the Public Library of Science. doi:10.1128/9781555817381.ch15.f1

Citation: Versalovic J, Highlander S, Petrosino J. 2015. The Human Microbiome, p 226-237. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch15
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Image of FIGURE 2

Differences in microbial composition by body habitat. The figure shows the relative abundances of six different bacterial phyla at eight different body sites. The relative abundances were obtained by next-generation DNA sequencing of 16S rRNA genes. Adapted from with permission from the Nature Publishing Group. doi:10.1128/9781555817381.ch15.f2

Citation: Versalovic J, Highlander S, Petrosino J. 2015. The Human Microbiome, p 226-237. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch15
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Image of FIGURE 3

Bacterial compositions at different skin sites. The relative abundances of different bacterial phyla and genera are depicted in terms of the type of skin site (dry, moist, or sebaceous). The data were generated largely by 16S rRNA gene sequencing of organisms on swab samples obtained from different skin sites. Adapted from with permission from Elsevier. doi:10.1128/9781555817381.ch15.f3

Citation: Versalovic J, Highlander S, Petrosino J. 2015. The Human Microbiome, p 226-237. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch15
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Basic terminology of the human microbiome

Citation: Versalovic J, Highlander S, Petrosino J. 2015. The Human Microbiome, p 226-237. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch15
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Predominant phyla in healthy individuals by body site

Citation: Versalovic J, Highlander S, Petrosino J. 2015. The Human Microbiome, p 226-237. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch15

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