colon bacteria research

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colon bacteria research

Postby George Becker Rust » Thu Jul 18, 2013 4:08 pm

where could I find information about the bacteria and bacteriophages present in the human digestive tract? specifically, information about the relative frequency of bacterial families and perhaps even individual species in the most prevalant familes (present not isolated preferably, if that is known..and also how such information is procured wouldn't hurt, but is unnecessary if the source is reliable) and bacteriophages, information about the physical conditions said bacteriophages can endure, and markers that they use to attach to the bacteria, markers common to many bacteria present in the digestive tract, and bacteriophages with a low serological specificity to said markers or who attach to a fairly common marker, etc... ultimately, I'm trying to select a phage for use as a vector in gene delivery, or at least find enough background so that i could write a report on possible options. I have attempted gale virtual reference library, Google, my local library, some online databases through my local library, but have only found information either too general or too specific for my use. Any help and advice on how to proceed with such research would be appreciated.
George Becker Rust
 
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Project Question: research into the feasibility and practicality of a medical treatment for the upcoming conrad spirit of innovation challenge (details omitted for obvious reasons)
Project Due Date: abstract officially due october 24
Project Status: I am conducting my research

Re: colon bacteria research

Postby SciB » Thu Jul 25, 2013 6:28 pm

Hi George,
Your questions are intriguing. I am somewhat familiar with the human gut microflora but I hadn't thought about the possibility of modifying it through the use of bacteriophages delivering DNA. I looked up which species are the most common in the gut and found a list in the Online Textbook of Bacteriology http://textbookofbacteriology.net/normalflora.html This chapter on human flora has a list of the most common bacteria found in and on the body and for the lower GI tract this includes Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, Bacteroides sp., Bifidobacterium bifidum, Lactobacillus sp., Clostridium sp., and Spirochaetes. Most of these bacteria are or can be human pathogens and cause disease if they get into the wrong place. Apparently they can survive in the gut without causing disease—usually--although they may be associated with chronic inflammation as occurs with irritable bowel syndrome. This is a huge and complex area of investigation and the data are far from complete.

You said you were interested in bacteriophages that could be used as vectors to deliver genetic material into the intestinal bacteria. The only phages I am familiar with are the ones that can infect E. coli such as T2, 4 and 6 and M13. The T-even phages are all lytic, however, and will destroy the E. coli cells. M13 is infectious but does not cause the bacteria to break up.

You did not say why you want to use a phage to introduce DNA into gut bacteria, but if you want the cells to survive then you need to use a non-lytic phage such as M13—at least for E. coli.

From what I remember of phages, they are quite specific for species of bacteria, so each species in the gut may have its own particular phages. You might be able to engineer one that would have more general specificity as a vector, but that would involve research more on the level of a PhD thesis than a science fair project.

If you post again with some specifics about what you plan to use the phage for, we could help you better to design a project. Just remember that working with human pathogens would require special training, permissions and access to a lab with a biosafety cabinet to work in http://www.sciencebuddies.org/science-f ... fety.shtml

Best wishes,

SciB
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Re: colon bacteria research

Postby George Becker Rust » Fri Aug 02, 2013 8:01 pm

By the deadline, my group is expected to produce an abstract detailing our proposed innovative product. In our abstract we are supposed to detail the problem which our product addresses and how it differs from the current technology which addresses it. For the sake of the competition my group is considering restricting our idea to an oral delivery of page which would insert the genes for the production of Alpha galactosidase A. The  intention is for this to be a product which would act as an anti-flatulent and aid for gastrointestinal symptoms which however would be long-term rather than requiring repeated oral consumption as something like beano. Clearly there are possible applications for many enzyme deficiencies which can be treated by oral supplement. If our group could do well in the competition, we could gain access to resources which might help us pursue realization of this idea...We are not firmly set on a decision of Alpha galactosidase A, originally we were considering insulin, so that diabetics might not have to repeatedly needle themselves, but we thought that this was an avenue which had complications in the form of regulation: getting the insulin production to correlate with sugar levels may be difficult considering that human regulatory genes may not function in the bacteria. Again, any help would be appreciated. Thank you for the assistance thus far. We are to be coached by Mr.Walt erhardt, one of our chemistry teachers at the Battle Creek area math and science center. He may be of some assistance in assisting us. His email is werhardt@bcamsc.org. My group currently lacks a name, however I am the spokesperson, so on the behalf of the rest of my tentative group, thank you.
George Becker Rust
 
Posts: 2
Joined: Wed Jul 17, 2013 4:24 pm
Occupation: Student
Project Question: research into the feasibility and practicality of a medical treatment for the upcoming conrad spirit of innovation challenge (details omitted for obvious reasons)
Project Due Date: abstract officially due october 24
Project Status: I am conducting my research

Re: colon bacteria research

Postby SciB » Tue Aug 06, 2013 5:05 pm

Hi George,

Using bacteriophage to deliver the alpha galactosidase gene to the gut as a gas preventive is a very interesting and innovative idea, but I have one major concern. How are you going to determine how much of the phage survives its journey through the digestive tract? How much will be digested by proteases and nucleases in the stomach and small intestine? I think the idea with Beano was that it would break down the complex sugars in the stomach before the enzyme itself was digested. Your idea is to put the alpha-gal gene into some bacteria in the intestine so that they produce the enzyme themselves, correct?

In order to get the phage to the intestine intact, I think you would have to package them in a pill or capsule with an enteric coating that a person could swallow and that would resist stomach acid and only break down and release the phage at pH 7 in the intestine.

You could test your formulation in a mock-up of the stomach containing HCl at pH 1 and see how long it would resist breakdown, then try it at pH 7 to show that it breaks down and releases the phage. Your proof would have to include an experiment with your target bacteria to prove that the phage after exposure to the ‘stomach’ and the ‘intestine’ could then pass the alpha-glycosidase gene into the bacteria and have them produce enzyme that breaks down galactosidase.

If you can do all that successfully, you will definitely have a good chance at winning the science fair competition!

Let us know if you have more questions.

Best wishes,

Sybee
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Posts: 482
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