
A first look at my microbiome - colevscode
http://biomehacking.brace.io/articles/firstresults/
======
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.

~~~
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.

------
aroch
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.

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.

~~~
jere
>They're putting a shiny, appealing veneer over what amounts to homeopathy

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.

~~~
aroch
This may not be, but things like Soylent which claim to solve all your
nutritional and health needs by drinking it, are the equivalent of homeopathy
-- like say, drinking g tea made from the horn of rhino will make your virile.

~~~
jere
Well, I'm there with you on Soylent. And the at home FMT makes nervous as
well. What I don't get is the widespread notion that: self experimentation
makes you a nutter.

~~~
aroch
Self experimentation doesn't make you nutters, its performing invasive medical
procedures that involves the transfer of biologic waste from one person to
another with no clinical supervision that makes you nutters

~~~
logfromblammo
A little perspective, here, please. Humans sell lubricant specifically
marketed for introducing foreign objects to their lower digestive tract. We
also sell home enema kits without a prescription at local drugstores. You
don't need clinical supervision. At best, they could provide donor screening
to reassure you that you aren't going to give yourself a new disease. If you
know the donor, you could probably do at least as well just by observing them
for a period of time.

Putting someone else's poop in your colon is not that disturbing when you
realize that it already had your poop in it. It wasn't exactly squeaky clean
before the procedure.

And believe me, the guy squirting strange feces into himself as a personal
experiment has thought about this a lot harder than you. Even the guy doing it
for a bar bet has probably invested more doubt.

------
phy6
I'm going to create a Kickstarter to sell shit.

Pledge $5 or more: ___FMT Hall of Fame_ __Receive a used wipe, suitable for
bragging or framing (plus S &H).

Pledge $100 or more: [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)

Pledge $500 or more: ___FMT Classroom Educational Package_ __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.

Pledge $5000 or more: ___FMT Founders Club_ __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)

[http://en.wikipedia.org/wiki/Bristol_Stool_Scale](http://en.wikipedia.org/wiki/Bristol_Stool_Scale)

~~~
MatthewWilkes
I'm so proud of my university.

------
HillRat
While I'm a huge proponent of patient autonomy and knowledge, it's _really,
really, really_ 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.

~~~
colevscode
I agree, and I don't intend to encourage people to be casual about the risks
involved. But I'm also concerned about the possibility that this incredible
tool will become inaccessible.

~~~
HillRat
Agreed! Thankfully, the FDA backed off requiring IND applications for FMTs
last year, so the clinical burden is much less than was originally
anticipated.

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.

------
sciencerobot
The difference is well within the variation you'd expect from multiple
samples, extraction, PCR, sequencing, day-to-day.

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.

~~~
jp555
Do we know specific pro-biotic species that have been found to be
significantly more beneficial than the rest? How do we know?

Does "pro-biotic" refer only to beneficial prokaryotic organisms or are there
known beneficial "pro-biotic" foreign eukaryotes?

~~~
blacksmith_tb
There are some eukaryotes, yes, e.g. Saccharomyces boulardii.

~~~
jp555
Ah the yeasts! I recently heard that middle-eastern ancients regularly rubbed
old-bread on wounds to speed recovery. Probably more for penicillin mold, but
maybe the yeasts were at play as well?

------
Zikes
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.

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://www.nczonline.net/blog/2014/04/02/i-have-lyme-disease/)

------
TallGuyShort
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.

~~~
lotsofcows
I'm concerned with the average as a concept. Is the average calculated from
every user of uBiome? Does that make any sense? Surely there are significant
changes between the sexes? What about race, social group, location, etc?

~~~
njbooher
Microbiome research is still very new. I'm surprised there's a service
already.

------
jarin
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.

~~~
TallGuyShort
Yeah they're missing the <em> </em> around "close" in "a close friend acting
as the donor".

------
gone35
Ok in the interest of harm reduction and informed consent, please please read
the following two links if you are thinking about undergoing FMT:

[http://thepowerofpoop.com/epatients/fecal-transplant-
faqs/](http://thepowerofpoop.com/epatients/fecal-transplant-faqs/)

[http://thepowerofpoop.com/epatients/is-fecal-transplant-
for-...](http://thepowerofpoop.com/epatients/is-fecal-transplant-for-you/)

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.

------
myblake
Hacker news: where your DIY at home poop transplant only upsets people because
of an incorrect claim of statistical significance.

------
dsugarman
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.

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.

~~~
sakai
16S reads should be fine for basic characterization. The bioinformatics tools
for sequence classification of short reads from a full sequencing run have
also improved dramatically recently. Especially in terms of speed (100-1000X
improvements).

(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](https://helix.io)

------
simple10
"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.

------
giarc
Big question for you.... did you do anything prior to FMT to alter your flora?

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).

------
goodmachine
If you must do uncontrolled 'experiments' with your gut microbiome try food
before feces

[http://drbganimalpharm.blogspot.co.uk/](http://drbganimalpharm.blogspot.co.uk/)

------
callesgg
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.

------
scrumper
Goodness me. I have seen it all now. I do hope peer-to-peer poo sharing finds
its way into an episode of that new HBO Silicon Valley series.

------
bitJericho
So you made a blog about your poop. Good game, internet.

------
colevscode
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.

~~~
colevscode
After receiving several emails protesting the removal of the article, I
reposted it after editing out the parts that attempted to draw conclusions.
There's also a disclaimer at the top that warns about the danger of FMT.

------
zmanian
Did the site go down under load or taken down by creator?

------
shiftpgdn
Is this satire? Did he really have a friend poop into his butt on whim?

~~~
unwind
FMT is at least a real process, see
[http://en.wikipedia.org/wiki/Fecal_bacteriotherapy](http://en.wikipedia.org/wiki/Fecal_bacteriotherapy).
I don't think you quite captured how it's done in practice, though.

~~~
shiftpgdn
It's a real practice in hospitals with trained medical doctors. Not "in my
apartment with a close friend."

