In the 17th century, Antonie van Leeuwenhoek, the Dutch scientist known as the father of microbiology, developed microscopes capable of visualizing bacteria. Over the next three centuries, scientists became increasingly aware of the extensive presence of microbes throughout the environment. However, most of the species that could be seen could not be grown or studied in a lab. In the late 20th century, researchers developed new tools, including DNA sequencing, which determines the genetic makeup of an organism. This, in turn, allowed researchers to determine evolutionary relationships among the many microbial species.
At the start of the 21st century, further advances tremendously reduced the cost and effort required to conduct DNA sequencing. Simultaneously, technological advances drove down the cost of computing power. Techniques or technologies allowing direct sequencing of microbial DNA from entire microbial communities within specific environmental samples and the analysis of resulting data, collectively called metagenomics, have revolutionized our understanding of microbes in the environment. Today it is possible to extract all of the DNA from an environmental sample—encompassing all organisms present in the sample—sequence it rapidly, and apply sufficient computing resources to begin deciphering what all of the sequences mean. Metagenomics allows researchers to determine all of the genetic material—genes and other genetic elements—in a sample. Once all of the genes from a sample are known, they can be compared against databases containing gene sequences of known functions. With these tools researchers can match microbes with functions directly through their DNA.
Applications of metagenomics are many and varied. The growing field of bioremediation uses microorganisms to remove or detoxify pollutants. Metagenomics is being applied to the plastisphere (an ecosystem that forms in or on human plastic pollution) in an attempt to find genes that code for enzymes that might decompose plastics and provide a bioremediation solution to the massive plastic pollution challenge. The interactions of plants with microbes in the soil are being studied with metagenomics to determine better agricultural practices for increasing yields and crop nutrition and for decreasing the accumulation of toxic chemicals in plants. Metagenomics is also being used to improve human health. Sequencing the genome of the human gut bacterium E. coli has allowed for discoveries into the maintenance of a healthy ecosystem inside of the intestines. This research shown that E. coli produces enzymes and other chemicals used in digestion. Additionally, knowing the genome sequence has allowed for greater identification of individual species of beneficial bacteria, which helps with the identification of the harmful species.