Montag, 1. Mai 2017

Probiotics: does it bring anything?



The dysbiosis concept
As I wrote in my last post, there are several diseases which are supposed to be linked with an unhealthy gut microbiome. A recently common concept is the connection between dysbiosis – an unfavorable change in the composition of the microbial community – and health. It is likely that dysbiosis can provoke inflammations, obesity and diabetes[1]. A study by Ley et al. claims a connection between obesity and the ratio of Bacteroidetes in the gut microbiome[2].  
The question, if probiotics really are able to change the composition of a dysbiotic gut microbiome is discussed in the moment. Kristensen et al. investigated seven different studies on effects of probiotics on fecal microbiota[3]. In none of these the probiotics had a significant influence on the composition of the microbiota. Additional research is needed. Interesting would also be to research on the question, if probiotics can make the existing gut microbiome more resistant against disturbances.

Effects of probiotic organisms on gut microbiota and human health
The most frequently used microorganisms in commercial probiotic products are members of the genera Lactobacillus and Bifidobacterium but also Escherichia coli, enterococcus, certain Bacillus species, Saccharomyces boulardii and Saccharomyces cerviciae are employed[4]. There are several in clinical studies reported effects of probiotics with Lactobacillus or Bifidobacterium organisms such as lowering faecal enzyme activity, immune enhancing, tempering diverse sorts of diarrhea or balancing intestinal microflora [5]. Another interesting study showed that probiotics with Bifidobacteria can help to prevent inflammatory disorders by attenuating the gut permeability for endotoxemia. Endotoxemia are produced in order to a high-fat diet and can have inflammatory effects[6].

Probiotic cultures are claimed to have numerous of other effects on the human gut microbiome. For example they are able to change the metabolic properties of the indigenous microbes by competition for food[7]. Another possible effect is the changing of the microenvironment caused by the metabolic pathway outcomes of the probiotic organisms (e.g. cecal short-chain fatty acids, choline, ethanol)[8]. Probiotic organisms may are able to competitive exclude other (also pathogenic) microorganisms, they can act as a barrier on the gut epithelium or produce growth substrates (see Figure 1)[9].

Figure 1: Possible effects of probiotic organisms on human gastrointestinal microbiota


Should commercial be allowed to claim any positive effect of probiotic products?
The mechanisms of probiotic effects are still nowadays not completely understood. There are a lot more in vitro than in vivo studies and just few in human. So, the validity of most of the studies is not necessary given for the human organism.
As the knowledge on how probiotics effect our health is still really small I think commercial companies shouldn’t be allowed to claim any positive effect. I believe there is a great potential in biotics, but more in medications which are especially made for certain diseases. Probiotics in food are in my opinion to general. I rather believe in a necessity of studies, which investigate how our food behavior can affect our gut microbiome. Because the “probiotics” in natural, untreated food are free.



References

1          P. Hemarajata, J. Versalovic Effects of probiotics on gut microbiota: mechanisms of intestinal      immunomodulation and neuromodulation. (2013) Ther. Adv. Gastroenterol. 6, 39–51.

2          R. E. Ley, P. J. Turnbaugh, S. Klein, J. I. Gordon Microbial ecology: Human gut microbes associated with obesity. (2006) Nature. 444, 1022–1023. 

3          N. B. Kristensen, T. Bryrup, K. H. Allin, T. Nielsen, T. H. Hansen, O. Pedersen Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials. (2016) Genome Med. 8, 52. 

4          Y. Ringel, E. M. Quigley, H. C. Lin Using Probiotics in Gastrointestinal Disorders. (2012) Am J Gastroenterol Suppl. 1, 34–40. 

5          W. H. Holzapfel, P. Haberer, J. Snel, U. Schillinger, J. H. . Huis in’t Veld Overview of gut flora and probiotics. (1998) Int. J. Food Microbiol. 41, 85–101. 

6          P. D. Cani, N. M. Delzenne Interplay between obesity and associated metabolic disorders: new insights into the gut microbiota. (2009) GastrointestinalEndocrine Metab. Dis. 9, 737–743. 

7          J. L. Sonnenburg, C. T. L. Chen, J. I. Gordon Genomic and Metabolic Studies of the Impact of Probiotics on a Model Gut Symbiont and Host. (2006) PLOS Biol. 4, e413. 

8          F. J. Martin, Y. Wang, N. Sprenger, I. K. S. Yap, T. Lundstedt, P. Lek, et al. Probiotic modulation of symbiotic gut microbial–host metabolic interactions in a humanized microbiome mouse model. (2008) Mol. Syst. Biol. 4,. 

9          P. W. O’Toole, J. C. Cooney Probiotic Bacteria Influence the Composition and Function of the Intestinal Microbiota. (2008) Interdiscip. Perspect. Infect. Dis. 2008, 1–9.

Donnerstag, 30. März 2017

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.

Samstag, 11. März 2017

4.4 Are micropropagated plants genetically identical and stable?




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

Several researches which examine clonal fidelity use the same two approaches: ISSR (inter simple sequence repeat) and RAPD (Random Amplification of Polymorphic DNA) (Alizadeh & Singh, 2009; Rawat, Rawat, Mehrotra, Chandra, & Nautiyal, 2013; Yadav, Aggarwal, & Singh, 2013). Therefore I consider these two methods as the common way to examine this issue.



For which reasons is mass propagation of Gloriosa such a promising technique and genetic fidelity so important?


Gloriosa is an old medicine plant which has been used for a long time in both Africa and Asia. The plant contains an alkaloid called colchicine. This substance is able to inhibit mitosis and is used to treat acute gout (Bajaj, 2012). Gloriosa is more and more used to produce colchicine through mass propagation (Yadav et al., 2013). Since it is used for medication it is important that the substances of content of the plant stay the same.



Explain the terms somaclonal variants, PCR, Primer, amplification, genetic markers. 

 


Somaclonal variants

Somaclonal variants are new genetic different cells which appear randomly when cells reproduce themselves. This happens particularly when the cells are in vitro clonal propagated.(Jaligot et al., 2011)  


PCR

Polymerase Chain Reaction (PCR) is a method to copy pieces of DNA. That for the DNA is heated to separate the twin strings. Then it is blended with synthetic primers which attach to certain areas of the single strings. Then enzymes extend the starters until there is another double string. (Duran, 2000)


Primer

A Primer is a short piece of single stringed DNA which attaches to a certain area of a single string of DNA. It is the starting point for the DNA polymerase to build the second string.(‘Primer, Starter | Biologie-Definitionen online’, 2013)


Amplification

Amplification means the multiplication of DNA fragments by artificial copying (‘DNA amplification’, 2003).



Genetic Marker

A sequence of DNA which is located on a known place of the chromosome (National Institutes of Health, n.d.).



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


Yadav et al. (2013) confirm, that these ISSR and RAPD are convenient to prove genetic stability of mass propagated Gloriosa. As in so many studies (see question 1) these are the preferred methods to prove genetic fidelity, I assume that they are save enough.





Literature:


Alizadeh, M., & Singh, S. K. (2009). Molecular assessment of clonal fidelity in micropropagated grape (Vitis spp.) rootstock genotypes using RAPD and ISSR markers. Iranian Journal of Biotechnology, 7(1), 37–44.


Bajaj, Y. P. S. (2012). Medicinal and Aromatic Plants II. Springer Berlin Heidelberg. Retrieved from https://books.google.ch/books?id=kofuCAAAQBAJ


DNA amplification. (2003). Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health. Retrieved from http://medical-dictionary.thefreedictionary.com/DNA+amplification


Duran, E. A. (2000, April 1). Wissenschaft im Alltag: Die Polymerase-Kettenreaktion. Retrieved 11 March 2017, from http://www.spektrum.de/magazin/wissenschaft-im-alltag-die-polymerase-kettenreaktion/826243


Jaligot, E., Adler, S., Debladis, É., Beulé, T., Richaud, F., Ilbert, P., … Rival, A. (2011). Epigenetic imbalance and the floral developmental abnormality of the in vitro-regenerated oil palm Elaeis guineensis. Annals of Botany, 108(8), 1453–1462. https://doi.org/10.1093/aob/mcq266


National Institutes of Health. (n.d.). Talking Glossary of Genetic Terms. Retrieved from https://www.genome.gov/glossary/index.cfm?id=86


Primer, Starter | Biologie-Definitionen online. (2013, March 17). Retrieved 11 March 2017, from http://www.biologie-lexikon.de/lexikon/primer.php


Rawat, J. M., Rawat, B., Mehrotra, S., Chandra, A., & Nautiyal, S. (2013). ISSR and RAPD based evaluation of genetic fidelity and active ingredient analysis of regenerated plants of Picrorhiza kurroa. Acta Physiologiae Plantarum, 35(6), 1797–1805. https://doi.org/10.1007/s11738-013-1217-x


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