What is Metagenomics?

Metagenomics is the study of microbes in their natural living environment, which involves the complex microbial communities in which they usually exist. The study examines the genomic composition of an entire organism, including each of the microbes that exist within it. It is an important concept for the microbes and the host to be thought of as interdependent and observed as a community, rather than considered to be separate entities.

Metagenomics-Biology Beyond the Microscope (Mississippi Metagenomics at UMN)

Microbes of earth

Microbes are essential for all life on earth because they are involved with processes in the biosphere to convert key elements of life (e.g. carbon, nitrogen, oxygen, sulfur) into biologically accessible forms. These chemical cycles are dependent on microbes to continue and maintain environmental stability.

Human life is hence intricately linked with microbial communities, which are responsible for the supply of nutrients, metals and vitamins. Microbes are directly involved in the process of fermentation, remediation of toxins, nutrient extraction and food digestion.

Microbial communities and human health

Given the essential role that microbes play in the health of humans and animals on earth, it may come as a surprise that the overwhelming majority of the microbial population that resides within humans has not been observed and researched significantly in the past.

Saliva swab sample

This opens up a new playing field for research in the field of metagenomics. If we are able to deepen our understanding of the microbial communities that regularly interact with humans, such as those that reside inside the gastrointestinal tract, this may shed some light on the interplay between microbes and human health. Microbes may encode metabolic pathways that are essential for survival of human life, even though they do not exist in the genome of humans.

Changes in the levels of microbes that regularly interact with humans may be associated with causing some health conditions, such as inflammatory bowel disease (IBD), cardiovascular disease, eczema or cancer.

The microbes responsible for these changes are not likely to be the type of microbes that directly cause illness or infection. Instead, the more likely explanation is that the microbes and the human body ordinarily work together to successfully digest food, remove toxins from the body and prevent infection from taking over the body. If there is a change in the function of the microbe that is so closely involved with human health, this may translate to the presentation of a health condition in the affected human.

Metagenomics and research techniques

The field of metagenomics is relatively new because microbes have traditionally been studied in a laboratory-based setting, rather than within the host as a combined entity. Therefore, the current knowledge of microbes in their natural habitat is scarce.

Metagenomics aims to make advancements in environmental and clinical microbiology, despite significant barriers such as difficulty to make a culture and the genomic diversity of microbes. It is hoped that increased understanding of the nature of microbes in the environment could have a significant impact on other sciences and research areas, such as medicine, biology, biotechnology and ecology.

In this early stage of metagenomics, the research is primarily focused on non-eukaryotic microbes, although it is expected that the study will encompass all areas of biology in time.


  1. https://www.ncbi.nlm.nih.gov/books/NBK54011/
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351745/
  3. https://www.ucc.ie/en/
  4. https://www.igs.umaryland.edu/

Further Reading

Last Updated: Aug 21, 2023

Yolanda Smith

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Yolanda Smith

Yolanda graduated with a Bachelor of Pharmacy at the University of South Australia and has experience working in both Australia and Italy. She is passionate about how medicine, diet and lifestyle affect our health and enjoys helping people understand this. In her spare time she loves to explore the world and learn about new cultures and languages.


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