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)
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.
1) At t=0 2) At t=x [no transplant] 3) At t=x2 [after transplant]
The thing you actually need to compare is the variation between the difference of 1 and 2 and 1 and 3. The variation between 1 and 2 measures the general variation in your gut biome. So now you have a baseline of what to expect under "normal" variation. So, how does this compare to what you see after the transplant?
Beyond this, how do you control for literally everything in your life around both samples? Maybe you were sick? Maybe you'd been to the gym? Maybe you ate a banana? How do these things affect the microbiome? Without this kind of information its very difficult to draw any kinds of conclusions regarding the impact of a transplant.
As an analogy - lets say I don't know anything about night and day.
I look at my window at some time (say in the morning). It's light. I then write the sentence "LET THERE MY NIGHT" on my wall in marker pen at around 8pm and look at my window. Behold - it's night! So, from this I might conclude writing on my wall brought about the night.
ALL that being said, being curious and engaged in this type of thing is only good. The important thing to bear in mind is that without some thought to experimental design the conclusions drawn cannot really be described as conclusions. This is a great first post, but the determination of natural variation in the gut mirobiome is needed before the impact of the transplant can even be considered.
Until you know those, you will be unable to conclude anything from these numbers.
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.
Arguably, this is the oldest and most fundamental version of science.
You don't need to go to school for ten years to great your Magical Science Certificate in order to practice Science--you just have to be able to ask questions and try out random shit and share your results.
It's haphazard, but at least people here are trying, right? And if they're unfettered by the academic-industrial complex, so much the better.
It's haphazard, but at least people here are trying, right?
We should not encourage people to randomly experiment on themselves under the guise of "being a hacker" when those experiments can pose significant threat to life. Unscreened, random FMT can have a number of potentially life threatening outcomes; stool contain human serum, blood, lymphocytes, viruses and other biologics that can be harmful.
How is self experimentation equivalent to homeopathy? I don't get how giving a shit about your own health is equated so quickly with a specific nonsensical, pseudoscientific sham.
[1] http://www.urbandictionary.com/define.php?term=Polishing%20a...
Also not much "shoving" was involved. I'll do another post later that describes the process. It's pretty gross, but mostly due to the preparation. (I had to put shit in a blender and press the button) The actual administration is about as gross as using a suppository.
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The µBiome stuff is really quite cool, but we don't really have the clinical data to properly analyze the results (which is why they include investigational surveys into the mix, so they are advancing the state of knowledge out there). Comparing your microflora to population averages doesn't tell us much, and there may be very good reasons for deviations from the mean. Having a FMT performed from a clean donor probably won't have any significantly deleterious effects (my gut feeling -- be here all week, folks -- is that a full antibiotics course is far more serious in effects, and we usually bounce back fine from these), but right now we're just tweaking dials on a machine we don't properly understand.
Nonetheless, I love the fact that you're keeping this data on yourself! Self-quantification is a huge step in maintaining health, and I'd love to read more about what you're doing.
Also, you're probably better off trying to alter your gut microbiome through ingestion of probiotics.
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.
Does "pro-biotic" refer only to beneficial prokaryotic organisms or are there known beneficial "pro-biotic" foreign eukaryotes?
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.
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 15 years, and was frequently misdiagnosed with everything from depression to having an eating disorder.
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.
[1] http://www.nczonline.net/blog/2014/04/02/i-have-lyme-disease...
http://thepowerofpoop.com/epatients/fecal-transplant-faqs/
http://thepowerofpoop.com/epatients/is-fecal-transplant-for-...
The biggest medical risk of the procedure involves contracting an illness from your donor, so it is paramount 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.)
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 very 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.
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.
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.
(Plug) I just launched a site last week that demos this and links to a few other academic works in the field (check the FAQ): https://helix.io
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.
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).