Analyzing Gut Microbes and Diseases in Turkey

[Zeynel]

Hello, I hope this is the right forum to ask this question. I'm a layman who is very interested in the microbes that live in our gut. I want to initiate a citizen science project to relate gut microbes to known diseases. For instance, this research ties Lupus to gut microbes http://www.hcplive.com/conference-c...obiome-seems-to-have-role-in-triggering-lupus

I'm imagining to form a company.

My question is: What type of machinery would anyone who wants to identify gut microbes uses? I'm in Turkey and I want to find out if this test can be done here.

My other question is: It is possible to identify gut microbes by traditional lab methods as in a Comprehensive Stool Test without using DNA. İs this technique inferior to DNA method?

Also please remember that I know nothing about microbiology.Thanks.

 

[Chip]

The important thing to keep in mind about the human biome is that there are on the order of 10^5 species and at least 10^7 or 10^8 strains of microbes present. So whatever your methodology will be, some sort of high throughput set of methods will likely be warranted.

 

[Zeynel]

Thanks for the answer. Do you know how much of the 100,000 species are known? If we don't know them how do we know there are 100,000 species? And do you know the name of the equipment used to identify these microbes so that I can investigate if this analysis is being done in Turkey?

 

[jim mcnamara]

DNA sequencing uniquely identifies microbes. DNA in bacteria are largely circular structures called plasmids. FWIW: Human mitochondria have their own separate DNA inside them and it is in plasmid form.

A lot of microbes are known largely from their DNA, mostly because it can be really difficult to isolate in culture medium every species of bacterium or virus or whatever in a sample of soil or human gut contents. There are lots of them.

So, when you are sampling human gut contents via feces, you have to eliminate human DNA from mitochondria.

There are laboratories that provide the service to the medical research profession. I do not know of a desktop implementation that you could afford let alone maintain and run competently.

This link discusses the hope of sequencing human DNA, the full genome of a single person, for $1000 a person. It is a dream right now. But you can see what costs are like.

https://en.wikipedia.org/wiki/$1,000_genome - note the dicussion of reagent costs (chemicals required).

check out this for general information about gut flora species https://en.wikipedia.org/wiki/Human_Microbiome_Project

 

[Chip]

Thanks for the answer. Do you know how much of the 100,000 species are known? If we don't know them how do we know there are 100,000 species? And do you know the name of the equipment used to identify these microbes so that I can investigate if this analysis is being done in Turkey?

My exposure to this area comes from reading papers, ie. mostly reviews. My hunch is that if you try to study the microbiome in any detail you will encounter precipitously diminishing returns in terms of accuracy, usefulness, reliability, etc. As with anything else extremely complex, you face an inevitable paradox that the more you seek to know about it the less you will understand. This phenomenon has been noted in the literature with respect to the study of the tumor suppressor gene, p53 (look up Yuri Labeznik). And this phenomenon does not depend on economic limits; the more money you spend the more you will waste if you are going down an increasingly inefficient path. Sorry to burst your bubble, but the solution to your problem is most likely going to need to reduce down to some trick, if you can find one. Another thing: you referenced SLE, which is autoimmune in nature. The immune system is one of the most complex systems in the realm of biology--its the only non-reproductive system that undergoes substantial genomic rearrangements. So even if you could master any microbiological aspect of SLE, you still will have barely scratched the surface.

Read the story of Kary Mullis and the invention of PCR. The greatest advances in sciences are, in fact, works of art. You are going to have to find a trick. Granted luck favors the prepared, but you are going to need some luck in this endeavor.

 

[Zeynel]

So whatever your methodology will be, some sort of high throughput set of methods will likely be warranted.

Can you explain what you mean by this. Not sure I understand it.

 

[Chip]

Oh, I want to mention one more thing in reference to the fact that you are in Turkey. I've researched quite a few pharmacologic studies in Turkey, and had a few conversations with a brilliant medical researcher I know. There has been noted a phenomenon in Turkey of a requirement of increased doses of drugs required for efficacy, suggesting a fundamental set of metabolic differences in your geographic region relative to the rest of the world. I bring this up because it could possibly have bearing in your current endeavor there. Microbiologic species have on their cell walls and membranes and secrete substances that have physiological effects, but if people in Turkey metabolize these substances differently than do people in other parts of the world you will want to be aware of this. I know this info is tangential to your current microbiological species ID task, but I hope all of this helps.

 

[Chip]

Can you explain what you mean by this. Not sure I understand it.

You could start with a primer such as this one: http://www.sumanasinc.com/webcontent/animations/content/highthroughput.html

 

[Zeynel]

Granted luck favors the prepared, but you are going to need some luck in this endeavor.

Thanks, Chip for the series of answers. This was helpful. I'm still studying what you wrote but just to clarify what I want to do:

I will not be dealing with the biology side. The lab will do the analysis and will send us the names of the microbes found in the gut of that individual. I will build a database and analyze it to find relationships between diseases and microbes. For instance, I will pull all individuals with Lupus and compare their microbes to healthy individuals. In my original post Dr. Silverman found that "patients with SLE had microbiota that were less diverse. SLE patients displayed a significant increase in Proteobacteria and a decrease in Firmicutes." I hope to find the same thing by analyzing the database. We could do the same analysis for other known diseases. This is what I want to do. Does it make sense?

For this I would need to have access to a lab that does genetic sequencing in Turkey. So far I'm not sure if this is done in Turkey. Unfortunately, I wrote to several academic microbiologist asking this same question but none of them replied. So I appreciate you taking time to help.