Metagenomics: How We Can Use Soil to Find New Antibiotics

By Michelle Wheater

Antibiotic resistance is one of the biggest problems the medical community is facing today, and one most of us have heard a lot about. Antibiotic resistance is an unfortunate process in which infectious bacteria are no longer affected by the drugs commonly used to kill them. Antibiotic resistance makes infections extremely difficult to treat. New outbreaks of resistant infections are frequently talked about on the evening news, but not so often are solutions to this problem presented. The solution is not as easy as it sounds- to solve this problem we need new antibiotics. But creating new antibiotics is a complicated, costly, and time consuming process.

The majority of current antibiotics come from molecules naturally produced by bacteria. Most of the bacteria that produce these useful products live right under our feet, in soil. Soils have a complex ecosystem that many of us rarely even consider. It contains a seemingly endless number of bactria, many of which have not been discovered. One of the most useful orders of bacteria, for antibiotics, pesticides, and nitrogen fixation, are the Actinomycetes. The common antibiotics streptomycin, erythromycin, and vancomycin all come from species of Actinomycetes. These drugs work by inhibiting bacterial growth through stopping protein or cell wall production while leaving human cells unaffected. Luckily, actinomycetes are able to be grown in a lab. But there are a vast number of bacteria that can not be cultured in scientific settings, and therefore have not been discovered or researched, which is where metagenomics comes in.

Artwork by Vayl Sorensen

Metagenomics is the process of capturing genetic material directly from the environment. Metagenomics has revealed extensive biodiversity in soil that we have previously missed. Sequences of DNA from the environment are put into huge databases where they can be filtered and scanned. Most of the time these databases are scanned for sequences similar to one being researched. But with the newfound biodiversity of sequences being put into these databases, when scanning for possible antibiotic producing sequences, functional metagenomics is a better option. Functional metagenomics searches for sequences that serve a certain function, such as enzyme or antibiotic production. When screening common antibiotic agents, it is thought that metagenomic research would yield sufficient new antibiotic compounds and mechanisms.

There are other obstacles that metagenics has in relation to antibiotic discovery has, but the first one that needs to be tackled is discovery of new bacteria and antibiotic molecules. Metagenomics is a time consuming and costly process. Antibiotics do not provide the incentives to pharmaceutical companies that other drugs for chronic conditions do. Funding and support for metagenomics needs to be provided if we are to reap the benefits from it. And we need these new antibiotics if we are to stop the outbreaks of resistant bacterial infections that are on the rise.


Handelsman, Jo. "How to find new antibiotics: metagenomics could be the way to mine the soil beneath our feet." The Scientist, 10 Oct. 2005, p. 20+. Academic OneFile, Accessed 20 Sept. 2018.

Handelsman, J., Rondon, M. R., Brady, S. F., Clardy, J., & Goodman, R. M. (1998). Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chemistry & biology, 5(10), R245-R249.

Hugenholtz, P., Goebel, B. M., & Pace, N. R. (1998). Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity. Journal of Bacteriology, 180(18), 4765–4774.

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