Blog entry 2: The gut microbiome: its determination, composition and function

The definition of our human body as a “superorganism” is based on the fact that our body resides a large collection of microorganisms, which play an important role in the health of the human body. All the genomic elements of these microorganisms together are marked as microbiome. (1) For an analysis of the human genetics to the full extent, it is necessary to examine the genes in the human genome, as well as identify the microbiome (2). Most of the microbiota in the human body can be found in the gastrointestinal tract (1).

Determination of the gut microbiome

Traditionally, the investigation of microbial communities has been dependent on cultivation techniques. For the gut microbiome, these techniques do not provide satisfactory findings. A better approach to identify the composition of the gut microbiome is through culture-independent metagenomic investigations in combination with 16s rDNA sequence analysis. The aim of this method is to provide an extensive view of the whole genetics from a community, which is accomplished through the primarily random sequencing of all DNA and later sequencing of the 16s rRNA-encoding gene. (3) This method not only allows to determine how many, but also which microbes exactly are present in the given microbial community (4).

Structure and dominant organisms

To fully understand the impact of the gut microbiome on our health it is important to know how it is structured. For the most part the gut microbiome consists of bacteria, but there are also archaea, fungi, viruses and protozoa present (4). An average healthy adult houses more than 1000 species of bacteria, the phyla Firmicutes and Bacteroidetes being the most dominant (5). The highest density of organisms can be found in the lower gastro intestinal tract (6). The composition of the different species can vary greatly between different healthy people, but the species are likely stable throughout a healthy individual’s lifetime (5).

Function in the human body

Without microbial activities in the gut, nutrition and digestion would not be possible (5). The gut microbiome fulfils various metabolic tasks like the production of vitamins and the synthesis of essential and nonessential amino acids. Another important function of the gut microbiome is the production of antimicrobial compounds, so it play an important role in the development our immune system as well. In many different studies, it has been elaborated that there is an association between the gut microbiota and chronic gastrointestinal diseases and systemic metabolic diseases like diabetes and obesity. (7)

The importance of the gut microbiome in life

While researching for this blog entry, I came across a large number of different scientific papers about the influence of the gut microbiome on our body. One thing they all had in common was the conclusion that further investigation is necessary to fully understand the role of the gut microbiome. The findings of the research seem comprehensible to me and I do believe in a close relationship between the gut microbiome and our health. One of the remaining questions is whether we are able to influence the composition of our microbiome - and therefore our health - by the consumption of probiotic microorganisms and our diet in general.

References:

(1) D’Argenio, V., & Salvatore, F. (2015). The role of the gut microbiome in the healthy adult status. Clinica Chimica Acta, 451, 97–102. https://doi.org/10.1016/j.cca.2015.01.003

(2) Gill, S. R., Pop, M., DeBoy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., … Nelson, K. E. (2006). Metagenomic analysis of the human distal gut microbiome. Science, 312(5778), 1355–1359.

(3) Wang, W.-L., Xu, S.-Y., Ren, Z.-G., Tao, L., Jiang, J.-W., & Zheng, S.-S. (2015). Application of metagenomics in the human gut microbiome. World Journal of Gastroenterology, 21(3), 803. https://doi.org/10.3748/wjg.v21.i3.803

(4) Cénit, M. C., Matzaraki, V., Tigchelaar, E. F., & Zhernakova, A. (2014). Rapidly expanding knowledge on the role of the gut microbiome in health and disease. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1842(10), 1981–1992. https://doi.org/10.1016/j.bbadis.2014.05.023

(5) Shreiner, A. B., Kao, J. Y., & Young, V. B. (2015). The gut microbiome in health and in disease: Current Opinion in Gastroenterology, 31(1), 69–75. https://doi.org/10.1097/MOG.0000000000000139

(6) Robinson, C. J., Bohannan, B. J. M., & Young, V. B. (2010). From Structure to Function: the Ecology of Host-Associated Microbial Communities. Microbiology and Molecular Biology Reviews, 74(3), 453–476. https://doi.org/10.1128/MMBR.00014-10

(7) Bull, M. J., & Plummer, N. T. (2014). Part 1: The Human Gut Microbiome in Health and Disease. Integrative Medicine, 13(6), 17–22. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4566439/pdf/17-22.pdf