3.4: The gut microbiome: its determination, composition and function

Determination of the gut microbiome

Nowadays there are several approaches for the so called metagenomics studies, which means genetic studies on mixed environmental microbial communities without having them cultured [1]. Two methods are widely used. One of them is examining 16S ribosomal RNA which allows to identify the bacterial species. Therefore the 16S rRNA genes are amplified by using PCR primers. Then the genes are sequenced and compared to a reference database. However, this method is only suitable to identify microbes which are known before. In an alternative approach, the so called shotgun method, the whole present DNA gets amplified by using random primers. Afterwards it is sequenced to build a representative database. This method is more extensive but suitable for all microbiota. [2]

Structure of the human gut microbiome

Regarding the human gut microbiome there are two groups of microbes to distinguish. There are species like Escherichia coli which occur in all healthy adults, called core microbiota [3]. On the other site every healthy adults gut is colonized by over 1000 phylotypes, which vary in time and across populations [4]. The biggest part of these consist of bacteria, belonging to the phyla Bacteroidetes and Frimicutes [5]. The rest is composed of Actinobacteria, Proteobacteria, Veruccobacteria, methanogenic archae, eukaryotes (mostly yeasts) and viruses [6]. 

Functions of the gut microbiome

It is just in recent years that researchers found out that the gut microbiome has some more functions than just digestion. First of all bacteria are able break down nutrients out of food components, where the human digestive tract isn’t able to. Then studies point out that the gut microbiota can interact with the human immune system. It is likely, that they have an important influence on inflammatory processes and thus on diseases linked to them [7]. In addition to that effects on obesity, autoimmune diseases and type 1 diabetes are discussed [2].

It is undeniable, that our gut microbiome has an effect on our health. For the next few years I expect a lot of new conclusions regarding this issue. Researchers will find out, how big this effect is and how it comes off. However, it will be a lot of work due to the complexity of these interactions.

Despite the great potential of the examination of this issue one has to look critically on the results of existing studies. Several gut microbiome studies are performed with sterile rats or mice which are inoculated with different microbes. I ask myself, how much the conclusions of these researches are translatable on humans. Another point is the poor comparability among human individuals. Due to the fact that the gut microbiome differs a lot over populations and even over individuals, it is hardly impossible, to make general statements.

References

1 J. F. Petrosino, S. Highlander, R. A. Luna, R. A. Gibbs, J. Versalovic Metagenomic  Pyrosequencing and Microbial Identification. (2009) Clin. Chem. 55, 856. 

2 M. C. Cénit, V. Matzaraki, E. F. Tigchelaar, A. Zhernakova Rapidly expanding knowledge on the role of the gut microbiome in health and disease. (2014) Genome Funct. 1842, 1981–1992. 

3 C. A. Lozupone, J. I. Stombaugh, J. I. Gordon, J. K. Jansson, R. Knight Diversity, stability and resilience of the human gut microbiota. (2012) Nature. 489, 220–230. 

4 M. J. Claesson, O. O’Sullivan, Q. Wang, J. Nikkilä, J. R. Marchesi, H. Smidt, et al. Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine. (2009) PLOS ONE. 4, e6669. 

5 P. B. Eckburg, E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, et al. Diversity of the Human Intestinal Microbial Flora. (2005) Science. 308, 1635. 

6 A. Reyes, M. Haynes, N. Hanson, F. E. Angly, A. C. Heath, F. Rohwer, et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. (2010) Nature. 466, 334–338. 

7 A. B. Shreiner, J. Y. Kao, V. B. Young The gut microbiome in health and in disease: (2015) Curr. Opin. Gastroenterol. 31, 69–75.