From the article: "I was able to significantly affect my microbiome with an FMT"<p>A huge pet peeve of mine is people claiming "significance" when they have no such thing. You have two data points and no controls. Even a simple control like another data point to see natural variation in your microbiome without an FMT is not present. Or sequencing a gut sample from your friend to show your sample moved in line with his (although in this case, since you moved toward the mean of the population, reversion to the mean is just as likely an explanation)<p>Catching up on the microbiome literature (I actually used to work on microbial communities, doing 16s rRNA sequencing on anaerobic digesters), it confirms my suspicion that your "significant" changes could easily be within the variation you would see naturally without an FMT.
This is probably an unpopular opinion but it seems to me that "SV culture" has taken to fetishizing "health hacking" with little to no medical training/background or support. See the recent SV craze with "health informatics hacking". They're putting a shiny, appealing veneer over what amounts to homeopathy and random self-experimentation.<p>Someone is going to say, "but they have all this data, like this guy from µBiome" -- he's not a doctor, he's not a trained scientist, he's a dude who is shoving fecal extracts from his friend up his bum and hoping the results are positive.
I'm going to create a Kickstarter to sell shit.<p>Pledge $5 or more:
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[EARLY BIRD] DIY kit: You'll get everything needed for a basic FMT, PLUS a single type 1 Bristol stool from one of our lead engineers.(plus S&H)<p>Pledge $500 or more:
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Join us for a PRIVATE squatting ceremony at a local nature reserve. You'll receive a fresh, hand wrapped type 3 or 4 Bristol stool from one of our members, plus a DIY implantation kit and hands on training.<p>Pledge $5000 or more:
<i></i><i>FMT Founders Club</i><i></i>
We'll fly you out to receive an entire Type 4 Bristol stool (smooth log) in person, along with a basic FMT course and PRIVATE implantation procedure. PLUS, we'll offer you the chance to donate your own stool samples to the FMT Master Catalog, for others to choose from. This is a two day event. (US & CAD only)<p><a href="http://en.wikipedia.org/wiki/Bristol_Stool_Scale" rel="nofollow">http://en.wikipedia.org/wiki/Bristol_Stool_Scale</a>
While I'm a huge proponent of patient autonomy and knowledge, it's <i>really, really, really</i> a bad idea to perform fecal microbiota transplantations at home, without medical equipment or training, and with an unvetted donor. I do hope that FMTs become an accepted part of medical practice -- the clinical results are more than encouraging -- but this kind of experimentation could go bad pretty fast.
The difference is well within the variation you'd expect from multiple samples, extraction, PCR, sequencing, day-to-day.<p>Also, you're probably better off trying to alter your gut microbiome through ingestion of probiotics.<p>Source: I am a PhD student research the human gut microbiome in connection with autoimmunity and have processed thousands of these samples using the exact same methodology as uBiome.
Methodologies aside, people really do have to take the majority of their personal health into their own hands. Most folks only see a doctor for a few hours in an entire year (much of that just sitting in reception) and rely on OTC self-medication for most minor issues.<p>There's a lot of criticism around people that self-experiment or self-diagnose, and it is indeed a potentially very dangerous practice, but the expense and fallibility of doctors can sometimes leave little alternative.<p>One example of this is Nicholas C. Zakas's recent account[1] of his discovery that he is afflicted by Lyme disease, has had it for the last <i>15 years</i>, and was frequently misdiagnosed with everything from depression to having an eating disorder.<p>The point is, regardless of education, nobody cares as much about your health as you do. Doctors deal with hundreds of patients, you get to focus on just one.<p>[1] <a href="http://www.nczonline.net/blog/2014/04/02/i-have-lyme-disease/" rel="nofollow">http://www.nczonline.net/blog/2014/04/02/i-have-lyme-disease...</a>
I'm no expert, but given the magnitude of the author's deviation from "average", I would have wanted to get several results over time to see typical variance before doing an FMT and trying to reason about the difference.
This is pretty fascinating, but I'm not looking forward to the conversation I'm eventually going to have to have with one of my fit friends about putting some of his poop in my butt so I can lose weight.
Ok in the interest of harm reduction and informed consent, please please read the following two links if you are thinking about undergoing FMT:<p><a href="http://thepowerofpoop.com/epatients/fecal-transplant-faqs/" rel="nofollow">http://thepowerofpoop.com/epatients/fecal-transplant-faqs/</a><p><a href="http://thepowerofpoop.com/epatients/is-fecal-transplant-for-you/" rel="nofollow">http://thepowerofpoop.com/epatients/is-fecal-transplant-for-...</a><p>The biggest medical risk of the procedure involves contracting an illness from your donor, so it is <i>paramount</i> that you properly screen your donor with appropriate tests. (I really, really hope OP did this; otherwise he might have put himself in substantial risk.)<p>Also note that the effectiveness of FMT for autoimmune disorders has so far been anecdotal and not nearly as robust as for C. difficile infection and, to a lesser extent, IBD/Crohn's disease. Be <i>very</i> aware of the risks and the conjectural/unclear nature of the claimed benefits. As of now clinics in the US only administer the procedure except for C. difficile infection, which is why some patients have resorted to at-home DIY transplantation. Please see the links above for specific guidelines on how to follow the procedure safely, should you decide to proceed.<p>Also as other posters have repeatedly pointed, the microbiome changes you report are well within variation/assay error and perhaps not as informative as you might expect.
I've worked on some metagenomics projects in the past, I admit I don't know too much about uBiome, but what I do know is that it is really hard to figure out what bacteria, archaea and fungi are in a given stomach.<p>consider that you can only cultivate a very small % of bacteria and archaea which means you can only find the genome of a given species that is living in a natural environment (often a very extreme environment). to figure out the genome, you have to sequence them all at the same time, but you can only read 1k-2k base pairs at one time, which means you need to bin these sequences into what you (educatedly) guess is the right organism and then sequence the genome. overtime, our understanding of these genomes should increase but I wonder what the current provable accuracy is using uBiome.
"Health hacking" is really more about the act of tracking. Most people I know involved in quantified self see benefits in being observant of their daily routines, food, exercise, etc. Drawing causations from the data is generally not possible, but learning more about yourself with tools like uBiome and WellnessFX can lead to better decision making on a daily basis. It can also help you learn how to ask the right questions from a doctor.
Big question for you.... did you do anything prior to FMT to alter your flora?<p>I work with a major researcher in FMT and actually act as a donor so I know a little about this. Patients receiving FMT typically receive a short course of vancomycin to rid the gut of bacteria (or as much as possible). It's like starting with a clean slate. Your gut is then more readily able to accept the donation. Without the vanco (or other abx) you are basically just throwing shit at more shit and hoping it sticks.<p>I think your results would really change if you had done this through a doctor and had a bit of abx prior to FMT (or even just an enema).
If you must do uncontrolled 'experiments' with your gut microbiome try food before feces<p><a href="http://drbganimalpharm.blogspot.co.uk/" rel="nofollow">http://drbganimalpharm.blogspot.co.uk/</a>
So basically he took another persons feces and put it in himself. Cause he had read about it in a completely different context. and it had almost no effect.
OP: Sorry all. I had hoped to raise awareness and encourage discussion, but I think there's a bigger danger that the way I presented this "experiment" will do more harm than good for the perception of FMT and at home microbiome exploration. I will consider revisiting once I've got my ducks in a row.