Blog entry 3: Probiotics - does it bring anything?

The last blog post contained the determination of the gut microbiome and its structure, as well as the assessment of its functions in the human body. This post is engaged with the influences of consumed probiotic bacteria on the gut microbiome and the human health.

In general, probiotics are described as living microorganisms, which have a beneficial impact to the human health when consumed in certain numbers (1). But can this benefit be scientifically proven?

Effects of probiotics on human health

It has been widely researched how the nutrition influences and changes the human gut microbiome. That the diet directly alters the composition of the microbiome has been proven by many different studies. Diet-induced obesity for example can be directly linked to the way the gut microbiome is structured. (2) The idea to deliberately wanting to improve the own health through diet seems comprehensible. Probiotics are one example for dietary supplements that should be constitutional when consumed regularly.

Probiotics (usually bacteria) survive the passage through the acid environment of the stomach and alter the microbial balance in the gut. They are known to crowd out potentially pathogenic bacteria that are already present. After that, the probiotic bacteria create an unfavourable environment for said pathogenic organisms. (3)

The most commonly used probiotics are Lactobacillus and Bifidobacterium. Although those are only two examples of a great number of species that can be used as probiotics. (4)

Some of the said beneficial effects of probiotic consumption include: (3)

• the increase of nutrient availability in fermented food and even the production of nutrients in the gut
• the reduction of symptoms from lactose intolerance
• the reduction of the severity of intestinal infections
• the reduction of blood cholesterol concentrations
• some protection against bowel cancer when probiotics are consumed long-term

Figure 1: Beneficial effects of probiotics on human health (4)

Probiotics in commercial use 

Despite many apparent advantages that come with the consumption of probiotics, it has to be considered that the knowledge of the gut microbiome is still very limited and therefore, the effects of probiotics cannot be distinctly defined. It is still unclear which parts of the microbial communities in our gut influence our health and how exactly they do so. (5)

In the end, even if probiotics have a positive influence on the gut microbiome, it has to be kept in mind that said bacteria are easily killed or destroyed during the process of making them available for consumers as dietary supplements (6). So even if probiotics are advertised on products in commercial use, the bacteria contained may not be alive anymore and won’t be beneficial for the gut microbiome. It would be important to know for the consumer how the product was processed and whether the bacteria are still alive when the product is consumed. However, Technologies in food productions are getting more and more advanced and it can be supposed that in the future there will be more and more possibilities in producing sensitive food with live probiotic bacteria.

References

(1) FAO/WHO. (2002). Guidelines for evaluation of probiotics in food. Report of a Joint FAO/WHO Working Group on Drafting Guidelines for the Evaluation of Probiotics in Food. Retrieved from http://www.who.int/foodsafety/fs_management/en/probiotic_guidelines.pdf

(2) 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

(3) Geoffrey P. Webb. (2006). Dietary Supplements & Functional Foods. Oxford: Blackwell.

(4) Lee, Y.-K., & Salminen, S. (Eds.). (2009). Handbook of probiotics and prebiotics (2nd ed). Hoboken, N.J: John Wiley & Sons. Retrieved from http://dx.doi.org/10.1002/9780470432624

(5) Nagpal, R., Kumar, A., Kumar, M., Behare, P. V., Jain, S., & Yadav, H. (2012). Probiotics, their health benefits and applications for developing healthier foods: a review. FEMS Microbiology Letters, 334(1), 1–15. https://doi.org/10.1111/j.1574-6968.2012.02593.x

(6) Watson, R. R., & Preedy, V. R. (2010). Bioactive Foods in Promoting Health: Probiotics and Prebiotics. Academic Press.

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

Blog entry 1: Are micropropagated plants genetically identical and stable?

Plant tissue culture or micropropagation has become a very important method to regenerate genetic identical clones of a plant in vitro and can result in preserving valuable genetic resources of threatened species. A problem in this process can be somaclonal variation among the clones. 

Picture 1: in vitro propagation of an orchid (B.Giger, 07.03.17)

The conventional way to prove the true-to-type nature of a clonal plant

RAPD (randomly amplified polymorphic DNA) and ISSR (inter simple sequence repeat) are the conventional methods to analyse the genetic stability of the generated plants. In these processes, the genomic DNA of the donor plant and the in vitro raised plants are compared to each other. (Saha et al., 2016)

Mass propagation of Gloriosa superba as a promising technique

The colchicine alkaloid contained in the tubers and seeds of G. superba has medical features and is antimitotically active. Due to the various usage, the plants containing colchicine are being exploited by many parties. This over-exploitation combined with the poor propagation of G. superba and its sensitivity to many pests are threatening to the species. Through mass propagation, it is possible to generate numerous new individuals of the species in a short time and thus cover the high demand of the plant and possibly save an endangered species. Genetic fidelity is very important, because especially for commercial use the generated plants mustn’t show any unwanted variations but should rather be homogenous to guarantee a certain standard of quality. (Yadav, Aggarwal, & Singh, 2013)

Terms

somaclonal variants	Somaclonal variants have their origin in in vitro cell and tissue culture. Normally, when cells ore tissue is amplified, the goal is to generate clones identical to the original cells or tissue. However, there can occur spontaneous genetic variability in the cultured cells and therefore, there are differences shown among the clones. The variations can be phenotypic or genotypic. (Orton, 1982)
PCR and amplification	PCR is short for polymerase chain reaction. It is a method used to synthesize a new strand of DNA, which is complementary to the original strand. This is possible by using DNA polymerase, which can add nucleotides to already existing 3’-OH-groups with the help of a primer. In the end, the synthesized DNA sequence can be multiplied various times and therefore is an amplification of the pre-existing DNA strands. (NCBI, 2014)
Primer	As mentioned above, the primers are needed for the polymerase chain reaction. It leads the DNA polymerase to the right place on the template strand, where it can begin the synthesis of new DNA nucleotides from the end of the primer.(NCBI, 2014)
Genetic markers	Genetic markers are alleles, which produce visibly different phenotypes and therefore their presence in an organism can be easily detected. (Griffiths et al., 2000)

Is the proposed method save enough to prove genetic fidelity of clonal propagated plants?

The assessment of genetic stability of micropropagated plant like G. superba through RAPD and ISSR analysis provides important information for the successful propagation of genetically identical and stable plants for commercial use. (Yadav et al., 2013)

References

Griffiths AJF, Miller JH, Suzuki DT, et al. An Introduction to Genetic Analysis. 7th edition. New York: W. H. Freeman; 2000. Mapping with molecular markers. Available from: https://www.ncbi.nlm.nih.gov/books/NBK21962/

NCBI. (2014). Polymerase Chain Reaction (PCR). Retrieved 10 March 2017, from https://www.ncbi.nlm.nih.gov/probe/docs/techpcr/

Orton, T. J. (1982). Somaclonal variation. California Agriculture, 8, 20–21.

Saha, S., Adhikari, S., Dey, T., & Ghosh, P. (2016). RAPD and ISSR based evaluation of genetic stability of micropropagated plantlets of Morus alba L. variety S-1. Meta Gene, 7, 7–15. https://doi.org/10.1016/j.mgene.2015.10.004

Yadav, K., Aggarwal, A., & Singh, N. (2013). Evaluation of genetic fidelity among micropropagated plants of Gloriosa superba L. using DNA-based markers — a potential medicinal plant. Fitoterapia, 89, 265–270. https://doi.org/10.1016/j.fitote.2013.06.009