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Chapter 13 : The Human Microbiome

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Abstract:

The human microbiome includes bacteria, viruses, and small eukaryotes, such as fungi, and this chapter focuses on the bacterial members of the microbiome. The Human Microbiome Project (HMP) aims at developing tools and resources for characterization of the human microbiota and to relate this microbiota to human health and disease. The goals of the jumpstart phase have been to sequence 900 reference genomes to provide a catalog of genomes for metagenomic studies, to sample at least 300 healthy adults between 18 and 40 years of age at five body sites, and to develop sequencing and analysis protocols for the samples derived from human subjects. The second phase of the HMP includes human microbiome studies that target particular disease states. In a recent study, four phyla comprised 92.3% of bacterial DNA sequences analyzed from multiple human sources, including hair, oral cavity, skin, genitourinary, and gastrointestinal tract. A study by Pei et al. showed that the distal esophageal microbiomes of four adults had compositions similar to that of the oropharynx, with the exception that no spirochetes were found in the esophagus. The chapter concludes by highlighting that pathogen discovery efforts will be enhanced by new metagenomics strategies, and these studies may uncover single etiologic agents of infections as well as relative shifts in groups of bacterial pathogens that may contribute to human disease.

Citation: Highlander S, Versalovic J, Petrosino J. 2011. The Human Microbiome, p 188-198. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch13

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Denaturing Gradient Gel Electrophoresis
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Restriction Fragment Length Polymorphism
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Image of FIGURE 1
FIGURE 1

Dendrogram showing results of cluster analysis of 40 taxa from subgingival plaque from 4,475 samples collected from 187 subjects. Distinct red, orange, yellow, blue, green, and purple clusters are highlighted. Reprinted with permission from ( ).

Citation: Highlander S, Versalovic J, Petrosino J. 2011. The Human Microbiome, p 188-198. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch13
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Image of FIGURE 2
FIGURE 2

Plot of double principal coordinate analysis of esophageal samples showing a distinction of type I (blue fill, healthy) and type II (yellow fill, diseased) microbiomes. Edge colors indicate host phenotype (green, normal; red, esophagitis; black, Barrett's esophagus). Adapted with permission from ( ).

Citation: Highlander S, Versalovic J, Petrosino J. 2011. The Human Microbiome, p 188-198. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch13
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Image of FIGURE 3
FIGURE 3

Principal coordinate plot of OTUs from the stools of 17 healthy subjects. The size of the circle corresponds to the number of sequences per OTU, and the color indicates the prevalence of OTUs among the 17 subjects. Inset: Venn diagram summarizing four studies of fecal microbiota from healthy donors compared with the core data set of 66 OTUs generated by Tap et al. ( ). The four studies are Eckburg et al. ( ), Manichanh et al. ( ), Gill et al. ( ), and Li et al. ( ). Numbers above the ovals indicate the number of core OTUs observed in the study. Numbers within the ovals indicate the number of OTUs that overlap with the core set of 66. Reprinted with permission from ( ).

Citation: Highlander S, Versalovic J, Petrosino J. 2011. The Human Microbiome, p 188-198. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch13
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Image of FIGURE 4
FIGURE 4

Abundance plot of bacterial groups from four phyla in skin samples from 10 healthy volunteers. (A) Sebaceous skin sites; (B) moist skin sites; (C) dry skin sites. Superscripts indicate the following phyla: 1, ; 2, ; 3, ; and 4, . Reprinted with permission from ( ).

Citation: Highlander S, Versalovic J, Petrosino J. 2011. The Human Microbiome, p 188-198. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch13
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Tables

Generic image for table
TABLE 1

Predominant phyla by body site

Phyla are listed in order of predominance inferred from the reference(s) cited.

Citation: Highlander S, Versalovic J, Petrosino J. 2011. The Human Microbiome, p 188-198. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch13

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