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Chapter 15
The Microbiome

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Figure 15–1. The human microbiome biogeography. Microbiota compositions vary per body site. In general, the microbial compositions
from the same sites over different individuals are more alike than the microbial compositions of different sites of the same individual.

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Figure 15–2. Intercommunication between the host and the gut microbiome. Gut microbes are known to communicate with the host
in numerous ways including through the production of metabolites, the modulation of the immune system, and altering gut permeability. In
turn, the host influences the gut microbiome in a variety of ways including altering the gut lumen environment through diet, and immune
modulation.

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Figure 15–3. From stool to statistics. Genetic material is extracted from fecal samples and prepared for sequencing. Digitized genetic
sequences are filtered for quality and compared to a database to identify which microbes the sequences belong to. From there, many
different multivariate statistical analyses can be performed, including principal component analysis, to characterize a sample and compare
it to other samples.

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Figure 15–4. Scientific tools and models to investigate the microbiome. An overview of the ways in which the interaction between
the microbiome and the host is investigated. Examples of techniques currently available include human clinical trials, conventional or
germ-free animal studies, intervention studies where humans or animals are given an FMT, anti-, pre-, pro-, or synbitoics and their effects
studied, followed by laboratory experiments designed to supplement the information garnered from the interventional treatment. Typically,
a combination of these techniques is used in modern research laboratories to reach a conclusion.

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Figure 15–5. Factors influencing the composition of the microbiome. A wide array of factors are known to influence the microbiome,
ranging from environmental factors to genetics. The most relevant are shown here.

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Figure 15–6. The effect of different diets on the composition of the gut microbiome. It has been shown that the relative abundances of
the main phyla of the gut microbiota differ greatly depending on the main types of foods consumed in the diet. Fish and oil are associated
with a higher relative abundance of Firmicutes, whereas plant-based food stuffs drive a greater relative abundance of Bacteroidetes.

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Figure 15–7. The microbiome is implicated in a variety of disorders. Much recent research has found evidence for a role for the
microbiome in many diseases including skin, metabolic, and cardiovascular disease, as well as cancer, infection, and neurodegenerative
and psychiatric disorders.

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Figure 15–8. Fecal microbiota transplantation (FMT) as a therapy. Stool from a healthy donor is collected and screened for safety.
Then, the FMT is given to the patient, sometimes after antibiotic-treated to wash out the old microbiota. The FMT restores host health by
instating a microbiome similar to that of the healthy donor.