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A first look at my microbiome

biomehacking.brace.io

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Re: A first look at my microbiome

#21

Post by JoeAltmaier »

sciencerobot wrote: post #16

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.

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.

Re: A first look at my microbiome

#22

Post by aroch »

angersock wrote: post #15
aroch wrote: post #5

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 µBiom…

"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…

    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.

Re: A first look at my microbiome

#23

Post by 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.

Re: A first look at my microbiome

#24

Post by aroch »

colevscode wrote: post #14
aroch wrote: post #5

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 µBiom…

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…

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.

Re: A first look at my microbiome

#25

Post by colevscode »

aroch wrote: post #22
angersock wrote: post #15

Earlier quoted context omitted.

"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…

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.

OP: I agree completely, unscreened "random" FMT would be a very bad idea. The donor in this case was definitely not random.

Re: A first look at my microbiome

#26

Post by 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.

Re: A first look at my microbiome

#27

Post by dsugarman »

JoeAltmaier wrote: post #21
sciencerobot wrote: post #16

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.

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.

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

Re: A first look at my microbiome

#28

Post by aroch »

jere wrote: post #20
aroch wrote: post #18

Earlier quoted context omitted.

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.

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.

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

Re: A first look at my microbiome

#29

Post by 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

Re: A first look at my microbiome

#30

Post by aroch »

colevscode wrote: post #25
aroch wrote: post #22

Earlier quoted context omitted.

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.

OP: I agree completely, unscreened "random" FMT would be a very bad idea. The donor in this case was definitely not random.

Knowing the donor, calling them your close friend, is not the same thing as medically screening both of you and the poo before the transfer.
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