welcome to the microbiome

Microbiome 101

By Jun Kim Ph.D.

As we tackle the myriad of challenges in society — healthcare, agriculture, environment, and energy — microorganisms are found to be everywhere and appear to have a very crucial role to play. For example, it is estimated that humans have as many microbes as human cells on their body 1, and 36% of the little molecules found in the human blood are caused by the human gut microbiome (a community of microorganisms that occupy a distinct region) 2. The human gut microbiome is of particular interest as there are numerous studies suggesting their important role in human physiology such as nutrient processing, stimulation of blood vessel formation, protection against pathogens, and regulation of fat storage 3.

It’s a gut party. The newly discovered quasi-organ.

The human gastrointestinal tract is an uncommon environment that accommodates varieties of microorganisms including micro-eukaryotic, bacterial and viral communities 4. The communication between this microbiome and the human host is crucial in determining the general health of the host which also includes illness probability. Metagenomics studies show the network of gene stockpile that exists within the human gut. The essential microbial gene set is believed to be almost 150 times larger than the human gene quota 5. This complex gene stockpile is said to be formed by genes coding for the production of amino acids, biosynthesis of vitamins and cofactors, degradation of xenobiotic compounds, etc. 5 Hence, the gut microbiome is armed with a metabolic capability that is similar to a quasi-organ operating within the gastrointestinal tract and thus, regarded as an external organ that aids the metabolic capability of the host. This metabolic capacity comes with several functions that the human host is not capable of performing such as the production of important vitamins that cannot be made by human cells.

I got it from my mama. What determines the makeup of an individual’s microbiome.

In addition to such a large number of gene sets involved, the fact that the interaction between the host and the gut microbiome is heavily influenced by a variety of environmental factors further complicates their relationship. At birth, microbes usually populate the gut, and the mother of the individual has a crucial part to play as the source of this process 4. After the population process is done, the progression and design of the gut microbiome is largely dependent on the age, diet, design of the individual, gender, geographic location, and the health status of the individual in question, whether in illness or not 4. For this reason, the findings in a group of individuals may be quite different from that of another set of individuals, especially when both sets of individuals have a different make-up genetically, different dietary habits, and lifestyles.

Ouch, my tummy hurts. Disease-associated with the microbiome.

Since there are many ways the microbiota can influence human physiology it is no surprise that microbiota changes have been associated with disease states. Experts have shown that the gut microbiome plays a part in the pathogenesis of inflammatory bowel disease by attacking and infecting the gut mucosa 7. However, the exact relationship between dysbiosis and disease pathogenesis is unclear in most cases at this time because of the inherent challenges in distinguishing between cause and effect. While dysbiosis may cause disease it should also be noted that the disease state can lead to changes to the microbiota through various mechanisms, including changes in eating habits and bowel function as well as through medications such as antibiotics 8.

Despite the complexity of the relationship between the host and the gut microbiome, this is an exciting time in the microbiome field. Recent advancements in sequencing technologies along with large-scale efforts now allow an analysis of the microbiome at the unprecedented detail. Some of the recent findings do clearly suggest the important role of the microbiota in particular diseases or conditions.


  • 1 Sender, R., Fuchs, S. & Milo, R. Revised estimates for the number of human and bacteria cells in the body.bioRxiv (Cold Spring Harbor Labs Journals, 2016).2 Hood, L. Tackling the Microbiome. Science(80-). 336, 1209–1209 (2012).
  • 3 Stappenbeck, T. S., Hooper, L. V & Gordon, J. I. Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc Natl Acad Sci USA. 99, 486, 222–227 (2012).
  • 4 Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature. 486, 222–227 (2012).
  • 5 Qin, J. et al. A human gut microbial gene catalog established by metagenomic sequencing. Nature. 464, 59- 65 (2010).
  • 6 Karlsson, F. H. et al. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature. 498, 99–103 (2013).
  • 7 Friswell, M., Campbell, B. & Rhodes, J. The role of bacteria in the pathogenesis of inflammatory bowel disease. Gut and Liver. 4, 295- 306 (2013).
  • 8 Shreiner, A. B., Kao, J. Y. & Young, V. B. The gut microbiome in health and in disease. Curr. Opin. Gastroenterol. 31, 69- 75 (2015).

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