Promises and Prospects of Microbiome Studies

Abstract

Since Anthony van Leeuwenhoek, first microscopic observations of the unseen microbiota and the more recent realization that little of the microbes in the biosphere are known, humans have developed a deep curiosity to fully understand the inner workings of the microbial realm. Our ability to characterize the complexity of microbial communities in their natural habitats has dramatically improved over the past decade thanks to advances in high-throughput methodologies. By eliminating the need to isolate and culture individual species, metagenomics approaches have removed many of the obstacles that hindered research in the ecology of mixed microbial consortia, providing valuable information about the diversity, composition, function, and metabolic capability of the community.Microbes are the unseen majority with the capability to colonize every environment, including our bodies. The establishment and composition of a stable human microbiome is determined by the host genetics, immunocompetence, and life-style choices. Our life-style choices determine our exposure to many external and internal environmental factors that permanently or temporarily can influence our microbiome composition. Figure 10.1 illustrates some of the life-style-related factors that might influence the microbiota of the skin, mouth, and gut. It is not limited to what we carry, touch, breath, and eat. Other dispersal vectors include secretion, excretions, aerosols, air flow, animals, moving surfaces, water, beverages, food, contact, wind, tools, toiletry, and others. These influence the microbiome membership, who are present, and they have the ability to participate in the microbiome dynamic within an environment. The establishment of a microbial community is dependent on many environmental factors, including pH, temperature, altitude, weather, soil type, nutrient availability, relative humidity, air quality, pollutants, microbial competitors, and others. In other words, we are superorganisms interconnected with other living forms on this Earth. 146 Metagenomics for MicrobiologyFig. 10.1. Microbiome of modern humans is influenced by life-style choices.During everyday life, humans are exposed to many external and internal environmental factors that can influence the composition of their microbiome. The human microbiome is here represented by the microbiota of the skin, mouth, and gut, and next to each body site a series of environmental modifiers. Some of these modifiers, such as general health, diet, medications, and stress, can affect the microbiota of more than one body site, but others, such as toothbrush and toothpaste, can directly modify the microbiota of only one body site. Promises and Prospects of Microbiome Studies 147The exploration of the microbial worlds uncovered the extreme microbial diversity throughout the biosphere, from hydrothermal vents on the ocean floor to the intestinal tract of animals. In addition to metagenomics, other technologies including metatranscriptomics, metaproteomics, metabolomics, and metalipidomics can provide...