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Let's assume that Joe has done some investigation on Internet and wants to see, if pro-biotics would help him. Now he goes to amazon.com and buys a pro-biotic product with excellent average rating. Note that not all of the reviews are from "Amazon Verified Purchaser" for the specific product, but you got the point that it sound convincing that other people claim to benefit from the product.

So validity of Joe's pro-biotic experiment starts from pro-biotic supply chain. What are the steps in his pro-biotic experiment where experiment could go wrong; and what are the precautions he can take to make his experiment successful - either prove or disprove their benefits?

In the answer I seek something between lines (feel free to reuse these points to make your answer whole):

  1. Joe should be confident that seller is selling the real thing and not candies. Are there any regulations that ensure that there is no fraud going on at this step from Over-the-Counter seller? How common is such fraud by sellers? Have there been any studies?
  2. The bacteria might die during shipping before Joe actually received his pro-biotics, for example, because of temperature changes. Obviously responsible seller should know how his merchandise should be shipped.
  3. Joe should probably not take pro-biotics together with other drugs or even together with other pro-biotics, because they might kill each other.
  4. There already could be some bacteria living in Joe's body that immediately kills "good bacteria" in pro-biotics without even making it.
  5. And most important - The initial hypothesis found by Joe on Internet about "good bacteria" in pro-biotics was wrong in the first place. Is there a website that I can check with convincing research that has studied how each bacteria affects our body as a whole?

Also, would it be worth to grow culture of pro-biotics at home to make sure that there is bacteria in the first place? How hard that would be? We have microscope at home.

The reason I am asking this is because a person very close to me is super excited about pro-biotics so that it starts to affect my life. I just want to get opinion from people in the biology field on how skeptical they are about DIY people doing such pro-biotic experiments at home. I am not sure yet whether I should support this person or try to talk out of this. It seems that this person has been reading a lot on Internet about this subject so it is not easy for me to argue back.

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    $\begingroup$ The supplement market in the United States is regulated by the Food and Drug Administration, however, they are not required to prove that their products work as they are usually sold as a food supplement and not as a medicine. As such, their clinical studies, if done, come under little scrutiny. Also there is a very small number of the species that make up the human microbiome that can be cultured outside of the human GI tract. A healthy diet is likely a better solution, unless of course "Joe" has a medical condition such as IBD and can find a Doctor willing to perform a fecal transplant. $\endgroup$ – AMR Dec 16 '15 at 1:19
  • $\begingroup$ @AMR With "Also there is a very small number of the species that make up the human microbiome that can be cultured outside of the human GI tract." did you try to imply that it is impossible to make pro-biotic supplements in the first place, because most species of good-bacteria would die right away once packed in pro-biotic capsules? I.E. suggesting that pro-biotic suppelement claims for that kind of bacteria would be scam? Is there somewhere a catalog of bacteria that would identify these kind of bacteria that can't be transferred via capsules? $\endgroup$ – Jonny Dec 16 '15 at 1:34
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    $\begingroup$ "Studies of Segmented Filamentous Bacteria biology have been hampered by the current absence of ex-vivo culture methods." -Ivanov II, Littman DR. Segmented filamentous bacteria take the stage. Mucosal Immunol. 2010;3(3):209-212 Nothing in science is ever impossible it is just a question of feasibility and whether someone has accomplished it. Obviously the ones in yogurt can be cultured, but many of the ones that they find genomes for in samples have not bet cultured, yet. The question of whether they can be ingested in capsule form and populate the colon is up for debate. $\endgroup$ – AMR Dec 16 '15 at 2:32
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    $\begingroup$ If you look at my answer here biology.stackexchange.com/questions/41478/… and here biology.stackexchange.com/questions/41415/… I have provided a lot of details about the microbiome and there are many references linked that you can research for yourself. $\endgroup$ – AMR Dec 16 '15 at 2:36
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    $\begingroup$ This is a list of the 539 journal articles that have been published as a result of the Human Microbiome Project. commonfund.nih.gov/publications?pid=16 $\endgroup$ – AMR Dec 16 '15 at 2:41

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