CH391L/S13/Probiotics

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=== Probiotics ===
=== Probiotics ===
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A human's mibrobiota , can be seen as an extended genome. This complex system of microbe-microbe interactions and host-microbe interactions is what allows an state of homeostasis, and when perturbed an state of dysbiosis ensues. Probiotics can alter a host's microbiome to move from the state of dysbiosis to homeostasis. Based on this we can suggest an ideal probiotic would try to achieve reestablishing the benefits in the context of a diet that includes a probiotic either as a supplement or a treatment to a disease. Nowadays this approach can take the form of a rudimentary fecal transplantation from diseased individuals to healthy ones, (include another example).
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A human's mibrobiota , can be seen as an extended genome. This complex system of microbe-microbe interactions and host-microbe interactions is what allows an state of homeostasis, and when perturbed an state of dysbiosis ensues. Probiotics can alter a host's microbiome to move from the state of dysbiosis to homeostasis. Based on this we can suggest an ideal probiotic would try to achieve reestablishing the benefits in the context of a diet that includes a probiotic either as a supplement or a treatment to a disease. Nowadays this approach can take the form of a rudimentary fecal transplantation from diseased individuals to healthy ones. Their approach to treat antibiotic-associated diarrea caused by Clostridium difficile infection was to assing patient to one of three treatments: 1) included a 4 day [[w:http://en.wikipedia.org/wiki/Vancomycin vancomycin]] treatment  , (include another example).
[[Image:Microbiome Source.png|thumb|right|400px]]
[[Image:Microbiome Source.png|thumb|right|400px]]
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**Another approach has been to genetically modify ''Streptococcus mutants'' by deleting lactate dehydrogenase gene and making it defficient in lactic acid production. In turn this same strain became an effector used to produce [http://en.wikipedia.org/wiki/Mutacin_1140 mutacin] which provided an advantage to other strains of ''S. mutans''. This strain was tested in gnobiotic rats was not reported to affect other indigenous flora except for other indigenous ''S. mutants'' strains that are associated with dental caries. <cite>Hillman2002</cite>
**Another approach has been to genetically modify ''Streptococcus mutants'' by deleting lactate dehydrogenase gene and making it defficient in lactic acid production. In turn this same strain became an effector used to produce [http://en.wikipedia.org/wiki/Mutacin_1140 mutacin] which provided an advantage to other strains of ''S. mutans''. This strain was tested in gnobiotic rats was not reported to affect other indigenous flora except for other indigenous ''S. mutants'' strains that are associated with dental caries. <cite>Hillman2002</cite>
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=== Frontiers in Probiotics : Genetic Modification ===  
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=== Genetic Modification of Probiotics===  
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Since probiotics are now being considered an alternative to antibiotics as antiobiotic-resistant strains of bacteria have become more common and bacteria that are present in diary products are not native to the human microbiota find a hostile environment where these are eliminated rapidly despite any benefit provided. Despite their beneficial therapeutic benefits that range from simple maintenance of the gut flora to causing tumor to regress this have not been widely implemented clinically. Their acceptance do have risks as we are still gaining knowledge about specific interactions ''in vivo''. Still it we could initially employ natural and artificial Gram positive strains, non-spore forming lactic acid bacteria to develop necessary approaches that could result in probiotics to treat diseases by genetically engineering or synthetically engineering new safe strains that could survive.
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*Food Grade Genetic Modification Systems
*Food Grade Genetic Modification Systems
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(Include explanation of food grade and plasmid modification)
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A Food Grade  and Generally Recognized as Safe Organism (GRAS) is a classification applied by the US Food and Drug Administration due to its long time use in food products. Most of the Lactococcus lactis strains contain, a GRAS organism, contain multiple plasmids that encode traits important for the food industry. These traits include sugar utilization, bacteriocins, and bacteriophage resistance.  Nowadays transfer of between these L. lactis strains occur via the method of bacterial conjugation. A second way to modify L. lactis, less common, is via what we know as [http://openwetware.org/wiki/CH391L/S13/DnaAssembly#Molecular_Cloning molecular cloning] of plasmids between GRAS strains, which has lead to the development of food grade vectors. A methodology used was isolating endogenous plasmids from ''L. lactis'' and separate isolation of useful markers from L.lactis strains that they could then put together into food grade expression Vectors <cite>Dunn2004</cite>
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Included in these are markers that permit their selection such as pVS40 plasmids(wide-host-range) or pWV01 plasmids (narrow-host-range) that contain a selectable marker that confers a new phenotype, i.e. utilizing a new sugar, or conferring metal resistance. A second way is to directly modify the probiotic at the chromosome level  as it allows for stable genetic modifications leaving no foreign DNA by employing thermosensitive plasmids. Finally also a genetic expression system has been developed for ''L. lactis''. An example of such an engineered strain is described in which an ''L.lactis'' strain in which by inactivating the aldB α-acetolactate decarboxylase gene increases α-acetolactate that is converted to diacetyl, which is the chemical responsible for butter's flavor. Other examples include of a LAB strain modification in which an heterologous gene from another one was introduced to increase the production of α-ketogluterate from glutamate in that is present in high levels in cheese. An so on so forth, yet examples like these are just baby steps in the advent of synthetic biology where much more could be done.<cite>Gueniche2009</cite>
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== Oversight of Probiotics ==
== Oversight of Probiotics ==
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==='''United States Regulation of Probiotics'''===
==='''United States Regulation of Probiotics'''===
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Probiotics are currently regulated by the Food and Drug Administration (FDA)in one of the following ways; As a dietary supplement, in which case only a premarket notice to the FDA is necessary or as a drug in which case a premarketing safety, efficacy and approval by the FDA are required. Currently, most of the probiotics on the market fall under the umbrella of a dietary supplement, but situations where the number of infections and the severity of such cases are causing clinicians to evaluate their use as drug, as it's happening for '''Clostridium difficile''' infections. In such cases, Florastor ('''Saccharomyces boulardii''') a probiotic currently marketed as a drug is beneficial as it demonstrated its efficacy in reducing the recurrence of '''C. difficile''' when used in combination with standard treatment methods. Although cases in which Florastor has lead to fungemia,yeast present in the blood, have been reported, mostly in patients that were not receiving the treatment via introduction of live yeast from contaminated hands of a technician to a catheter site.  
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Probiotics are currently regulated by the Food and Drug Administration (FDA)in one of the following ways; As a dietary supplement, in which case only a premarket notice to the FDA is necessary or as a drug in which case a premarketing safety, efficacy and approval by the FDA are required. Currently, most of the probiotics on the market fall under the umbrella of a dietary supplement, but situations where the number of infections and the severity of such cases are causing clinicians to evaluate their use as drug, as it's happening for '''Clostridium difficile''' infections. In such cases, Florastor ('''Saccharomyces boulardii''') a probiotic currently marketed as a drug is beneficial as it demonstrated its efficacy in reducing the recurrence of '''C. difficile''' when used in combination with standard treatment methods. Although cases in which Florastor has lead to fungemia,yeast present in the blood, have been reported, mostly in patients that were not receiving the treatment via introduction of live yeast from contaminated hands of a technician to a catheter site. <cite>Venugopalan2010</cite>
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<cite>Venugopalan2010</cite>
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== iGEM 2009: Stanford's Approach to Probiotics ==
== iGEM 2009: Stanford's Approach to Probiotics ==
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#Venugopalan2010 pmid=21029521
#Venugopalan2010 pmid=21029521
#Hillman2002 pmid=12369203
#Hillman2002 pmid=12369203
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#Ahmed pmid=14573362
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#Keller2013 pmid=
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#Gueniche2009 pmid=20808516
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#Dunn2004 pmid=15610425
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</biblio>
</biblio>

Revision as of 13:05, 25 March 2013

Contents

Introduction

A probiotic (from the Latin, pro-, "in favor, for" and the Greek , biōtikós, "pertaining to life")refers to live microorganism that provides a benefit to the host, either directly or indirectly, by via interactions with the hosts cells or the host's microbiota. Although research for most of the the last century focused on establishing the fundamentals of what a probiotics is, most of the ongoing research focuses now aims to characterize the microbial communities that have co-evolved with humans, such as Human Microbiome Project that that aims at characterizing the microbial communities found in on the human body and analyzing their roles in our health and disease[1], specific benefits provided by each single organisms to prevent disease. For example, the use of fecal transplantation for antibiotic-associated diarrea [2].(provide actual citation for original paper and summarize.

Definition of a Probiotic Trough Time
Definition of a Probiotic Trough Time


Probiotics

A human's mibrobiota , can be seen as an extended genome. This complex system of microbe-microbe interactions and host-microbe interactions is what allows an state of homeostasis, and when perturbed an state of dysbiosis ensues. Probiotics can alter a host's microbiome to move from the state of dysbiosis to homeostasis. Based on this we can suggest an ideal probiotic would try to achieve reestablishing the benefits in the context of a diet that includes a probiotic either as a supplement or a treatment to a disease. Nowadays this approach can take the form of a rudimentary fecal transplantation from diseased individuals to healthy ones. Their approach to treat antibiotic-associated diarrea caused by Clostridium difficile infection was to assing patient to one of three treatments: 1) included a 4 day w:http://en.wikipedia.org/wiki/Vancomycin vancomycin treatment , (include another example).

(Include paper with E.coli Nissile)

    • Another approach has been to genetically modify Streptococcus mutants by deleting lactate dehydrogenase gene and making it defficient in lactic acid production. In turn this same strain became an effector used to produce mutacin which provided an advantage to other strains of S. mutans. This strain was tested in gnobiotic rats was not reported to affect other indigenous flora except for other indigenous S. mutants strains that are associated with dental caries. [3]

Genetic Modification of Probiotics

  • Food Grade Genetic Modification Systems

A Food Grade and Generally Recognized as Safe Organism (GRAS) is a classification applied by the US Food and Drug Administration due to its long time use in food products. Most of the Lactococcus lactis strains contain, a GRAS organism, contain multiple plasmids that encode traits important for the food industry. These traits include sugar utilization, bacteriocins, and bacteriophage resistance. Nowadays transfer of between these L. lactis strains occur via the method of bacterial conjugation. A second way to modify L. lactis, less common, is via what we know as molecular cloning of plasmids between GRAS strains, which has lead to the development of food grade vectors. A methodology used was isolating endogenous plasmids from L. lactis and separate isolation of useful markers from L.lactis strains that they could then put together into food grade expression Vectors [4]

Oversight of Probiotics

United States Regulation of Probiotics

Probiotics are currently regulated by the Food and Drug Administration (FDA)in one of the following ways; As a dietary supplement, in which case only a premarket notice to the FDA is necessary or as a drug in which case a premarketing safety, efficacy and approval by the FDA are required. Currently, most of the probiotics on the market fall under the umbrella of a dietary supplement, but situations where the number of infections and the severity of such cases are causing clinicians to evaluate their use as drug, as it's happening for Clostridium difficile infections. In such cases, Florastor (Saccharomyces boulardii) a probiotic currently marketed as a drug is beneficial as it demonstrated its efficacy in reducing the recurrence of C. difficile when used in combination with standard treatment methods. Although cases in which Florastor has lead to fungemia,yeast present in the blood, have been reported, mostly in patients that were not receiving the treatment via introduction of live yeast from contaminated hands of a technician to a catheter site. [5]

iGEM 2009: Stanford's Approach to Probiotics

The 2009 Stanford iGEM Team project centered on probiotics and Inflammatory Bowel Disease (IBD). IBD, as explained, is caused by an imbalance of two types of T-cells, Treg cells that immunosuppres the Th17 cells that cause the inflammation seen in patients. They suggest that an novel theraputic mechanism can be achieved by in vivo regulation of these cells. Their approach focuses in constructing two different Escherichia coli(E.coli) strains, each that would contain a distinct input/output cassette , each that is referred as a device. The first device would detect as input Nitric Oxide(NO), a byproduct of inflammation and Th17 proliferation, produces retinoic acid, that blocks further CD4+ T-cells differentiation into Th17 cells. The second device detects 5-Methyl tryptophan (5MT) as an input and produces Interleukin-6 to regulate Treg proliferation to regulate their immunosuppression response. Ideally depending on the balance between these two markers, if too much NO is sensed by Device 1 it would prevent inflammation. The opposite would also be true if the second device sences to much 5MT that would immunosuppress Th17 cell by blocking their differentiation.


Probiotics and the Media links

The Media perspective on Probiotics

References

  1. Gordon JI. . pmid:22674326. PubMed HubMed [Gordon2012]
  2. Borody TJ, Warren EF, Leis SM, Surace R, Ashman O, and Siarakas S. . pmid:15220681. PubMed HubMed [Borody2004]
  3. Hillman JD. . pmid:12369203. PubMed HubMed [Hillman2002]
  4. Liu CQ, Su P, Khunajakr N, Deng YM, Sumual S, Kim WS, Tandianus JE, and Dunn NW. . pmid:15610425. PubMed HubMed [Dunn2004]
  5. Venugopalan V, Shriner KA, and Wong-Beringer A. . pmid:21029521. PubMed HubMed [Venugopalan2010]
  6. Kinross JM, Darzi AW, and Nicholson JK. . pmid:21392406. PubMed HubMed [Kinross2011]
  7. Bengmark S. . pmid:9505873. PubMed HubMed [Bengmark1998]
  8. pmid= [Keller2013]
All Medline abstracts: PubMed HubMed
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