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.
