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A first look at my microbiome

biomehacking.brace.io

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Re: A first look at my microbiome

#41

Post by colevscode »

cowsandmilk wrote: post #26

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…

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.

Re: A first look at my microbiome

#42

Post by awalton »

aroch wrote: post #18
jere wrote: post #13

Earlier quoted context omitted.

>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.

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.

Soylent claims to have every dietary macro-nutrient necessary for maintaining life. And it's pretty simple to look at it and say, "yep." It meets that claim perfectly as we understand macro-nutrients.

The problem is, there may be more to us than just "add macronutrients." We might need things like micro and nanonutrients. We might need variations in the kinds of proteins. The bacteria in stuff we eat might be the key to keeping us healthy in the long term. But how are we ever to know any of this unless someone studies it?

That, in absolutely NO WAY, should be misconstrued with homeopathy, which is absolutely bullshit about water "remembering" molecules that used to be in it.

Re: A first look at my microbiome

#44

Post by logfromblammo »

aroch wrote: post #28
jere wrote: post #20

Earlier quoted context omitted.

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

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.

Re: A first look at my microbiome

#45

Post by logfromblammo »

jere wrote: post #13
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…

>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.

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.

Re: A first look at my microbiome

#46

Post by computer »

colevscode wrote: post #41
cowsandmilk wrote: post #26

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…

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.

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.

Re: A first look at my microbiome

#47

Post by sakai »

dsugarman wrote: post #23

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 environ…

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

Re: A first look at my microbiome

#48

Post by sakai »

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.

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.

Re: A first look at my microbiome

#49

Post by logfromblammo »

aroch wrote: post #30
colevscode wrote: post #25

Earlier quoted context omitted.

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.

But it is thousands of dollars cheaper, which is kind of the whole point. People wouldn't be doing this themselves [as often] if genuine elective medical treatments were not priced out of reach.

Re: A first look at my microbiome

#50

Post by 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.
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