[cowsandmilk]

From the article: "I was able to significantly affect my microbiome with an FMT"

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.

[alexholehouse]

THIS. One hundred times this. For these results to be in any way meaningful you need to conduct the experiment three times (and, three times with one person isn't actually enough to actually pull statistically meanigful results from, but one step at a time).

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.

[tel]

I felt this way as well, though it'd be interesting to figure out the information that went into the "normal" range for bacteriodete/firmicute proportions to see how what kind of stability comes from that range is as well.

[colevscode]

OP: Thanks, removed the word "significant". I can't make any claims about the results yet. The donor sample is coming in soon so I will be able to make that comparison.

[computer]

You need to know standard deviations: the standard error of the measuring device (from Biome), the standard deviation within a subject (i.e. between measurements on different places, different times in one person) and between subjects.

Until you know those, you will be unable to conclude anything from these numbers.

[colevscode]

I pulled all the language that attempted to draw conclusions. I had removed the entire article but I received several emails from people who weren't interested in my results, just wanted to know what I did.