A first look at my microbiome

http://biomehacking.brace.io/articles/firstresults/

by colevscode • 12 years ago

86 69 12 years ago

biomehacking.brace.io

HillRat2• 12 years ago

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.

colevscode8• 12 years ago

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.

HillRat2• 12 years ago

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.

rdmirza• 12 years ago

FMT is already used as a treatment for c. dif here in Canada.

jarin2• 12 years ago

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.

TallGuyShort2• 12 years ago

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

aroch7• 12 years ago

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.

jere2• 12 years ago

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.

aroch7• 12 years ago

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.

logfromblammo4• 12 years ago

Man, you're just not seeing it. This "experiment" was not done going by rigorous scientific protocols. We have no idea whether or not the results are due poo placebo effects.

colevscode8• 12 years ago

OP here: It's true I'm not a doctor or scientist. This isn't a rigorously designed experiment. Yes, I am hoping that the results are positive, but I don't have unrealistic expectations. Mostly I'm just interested in seeing what I can learn about myself.

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.

aroch7• 12 years ago

There's a reason FMT's require clinical care and they don't sell "FMT-at-home" DIY kits. Without careful screening of the donor and recipient, you risk severe consequences. Bloodbourne pathogens are a real and present risk with fecal matter on top of the microorganisms poo contains. What's healthy/works in one persons gut can be tremendously bad for anothers.

jarin2• 12 years ago

Oh god, that is much worse than I was imagining. I was picturing something like swishing your finger around in some poop and sticking it up your butt, which is still gross but probably tolerable. Once you said the word "blender", I'm out.

angersock• 12 years ago

"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.

aroch7• 12 years ago

    It's haphazard, but at least people here are trying, right?

No, no, no, no.

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.

ajcarpy20052• 12 years ago

Even assuming you START with random experimentation, you will end up with non-random feedback. And assuming even cursory logical competence, the results of experiments will be useful. Even doctors get better over time with experience and practice.

colevscode8• 12 years ago

OP: I'm not from uBiome. I'm a uBiome customer. I've had little interaction with the uBiome staff to date.

smoyer• 12 years ago

I really expected you to say that they were "polishing a turd"! [1] On the flip side, you have to admire people who are becoming actively involved in their health AND learning more about the basic functions of human anatomy. A long time ago, it was illegal to dissect cadavers and medical knowledge required committing a crime. Isn't it better for smart people (who in theory understand the risks) to be allowed to conduct even uncontrolled experiments?

[1] http://www.urbandictionary.com/define.php?term=Polishing%20a...

TallGuyShort2• 12 years ago

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• 12 years ago

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• 12 years ago

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

shiftpgdn2• 12 years ago

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

unwind• 12 years ago

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

shiftpgdn2• 12 years ago

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

quasque• 12 years ago

I thought so too, and was most amused at everyone taking it seriously. Now I'm not so sure, but equally entertained.

simple10• 12 years ago

"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.

sciencerobot2• 12 years ago

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.

JoeAltmaier• 12 years ago

I'm curious: I've always suspected 'probiotics' are ineffective, like scattering a few daffodil seeds into a field of weeds. Either not a significant quantity to compete, or just 'food for bugs' which feeds everything indiscriminately.

dsugarman3• 12 years ago

as someone with plenty of gastrointestinal issues, probiotics are a godsend

jp5552• 12 years ago

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?

sciencerobot2• 12 years ago

Lots of correlations and associations but no Koch's Postulate as far as I know.

blacksmith_tb• 12 years ago

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

sakai2• 12 years ago

Aside: would be very interested in connecting about a metagenomics project I've been working on. My email is in my profile if you want to reach out.

dsugarman3• 12 years ago

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.

aroch7• 12 years ago

They're doing 16S sequencing, so short reads are fine and still diagnostic

sakai2• 12 years ago

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

cowsandmilk• 12 years ago

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• 12 years ago

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• 12 years ago

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.

colevscode8• 12 years ago

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• 12 years ago

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.

phy6• 12 years ago

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

MatthewWilkes• 12 years ago

I'm so proud of my university.

goodmachine• 12 years ago

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

http://drbganimalpharm.blogspot.co.uk/

bitJericho• 12 years ago

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

colevscode8• 12 years ago

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.

colevscode8• 12 years ago

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• 12 years ago

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

myblake• 12 years ago

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

gone35• 12 years ago

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/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.

scrumper• 12 years ago

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.

callesgg• 12 years ago

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.

Zikes• 12 years ago

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...

giarc• 12 years ago

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).

A first look at my microbiome

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