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Introduction to the gut microbiome

Gut bacteria

I’ve got what in my gut?

You might have heard recent reports that humans are colonized by many microorganisms (a.k.a. microbe) and that there are ten times more microbial cells within our bodies than our own [1].  Most of these cells (bacteria, protozoa and fungi, as well as viruses) are organized into communities called microbiota, within a specific niche, e.g. the human gut [2]. Since the historical discovery of bacteria and their association with disease, they’ve typically been considered harmful. However, that view has changed considerably with more recent discoveries of the many balancing and beneficial effects of certain microbes. But before we dig deeper into the important benefits of these bacteria and the microbiota, let’s first review some key discoveries.

From microbe to microbiota to microbiome

The fact that microorganisms were part of the healthy human system was for the first time proven in the middle 1880s, when Theodor Escherich, an Austrian pediatrician observed a type of bacteria in the intestines of children having symptoms of diarrhea, as well as in intestines of healthy children. This bacteria was later named Escherichia coli [3]. Throughout the 20th century, a number of other microorganisms were isolated from the nasal passages, oral cavity, skin, gastrointestinal tract, and urogenital tract and characterized as part of the human microbiota. Just as in the case of the gut, both sick and healthy people harbor microbes in these various locations. Although these groups of organisms have been studied and considered in many ways, the unifying concept of a microbial community or microbiota (present even in healthy people), was developed primarily in the first decade of the 21st century [4]. In the second half of the twentieth century, biology was unified by the idea that life on earth as we know it is all based on nucleic acid (DNA and RNA). This gave rise to the conceptualization of the community as a collection of genetic material, which came to be called the microbiome. Since each microbial cell carries DNA (and RNA) of specific and identifiable sequences of 4 letters (A, C, G, or T), the microbiome allows for quantitative measurement of the abundance of each of the thousands of microbial species in the microbiota.

Knowledge of human microbiota and microbiomes expanded greatly with the launch of the Human Microbiome Project (HMP) in 2008, to catalog the human microbiome and to provide insights into novel genes and species. One primary aim of the HMP was to research and understand the role of microbes in human health and disease. More precisely, five body areas (i.e. skin, mouth, nose, colon, and vagina) from 300 healthy people were sampled in order to examine their microbiomes [5].

How do we analyze a microbiome?

Analysis of a microbiome sample begins with the collection of a sample, such as a stool sample (for determining the microbial composition of your gut). Since microbes are virtually everywhere in the world, it is important that a sample is collected relatively free of environmental contaminants. It is also important to preserve the microbial composition of the sample. Microbes grow and die under varying conditions, so we use special collection devices to ensure the microbial composition doesn’t change before the sample reaches the lab. The next key step is to decode the order of letters of the DNA in the sample. Using computational approaches developed specifically for this purpose, abundances of specific microbial species are inferred by the abundance of certain DNA sequences. Next-generation sequencing is the method used to determine the bacterial composition of a given sample. The application of this revolutionary technology to microbiome analysis is giving us new insights into human and animal health, and into our extremely complex relationship with the potentially harmful or beneficial critters that live in and on us [6].


[1] Singh, R. K., Chang, H. W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., ... & Bhutani, T. (2017). Influence of diet on the gut microbiome and implications for human health. Journal of translational medicine, 15(1), 73. 

[2] Schloss PD, Handelsman J. Status of the microbial census. Microbiol Mol Biol Rev. 2004;68(4):686–691.  

[3] Lederberg, J., & McCray, A. T. (2001). Ome SweetOmics--A Genealogical Treasury of Words. The Scientist, 15(7), 8-8. 

[4] Rogers, K. (2016, April 7). Human microbiome.

[5] Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007). The human microbiome project. Nature, 449(7164), 804.  

[6] Claesson, M. J., Clooney, A. G., & O'toole, P. W. (2017). A clinician's guide to microbiome analysis. Nature Reviews Gastroenterology & Hepatology, 14(10), 585.  

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