Optimizing the microbiome (gut flora)


#1

Hey all,

I’m hoping to do two things with this post:

1.To explain why I think the Soylent community should be thinking about dietary microbes.

and

(2) To announce my own solution to this problem.

So without further adeu, here’s #1 from above:

Most nutrition information, and the probiotics commonly found in stores, were created before metagenomics and high throughput sequencing. Without metagenomics you are basically studying the gut strain by strain, with metagemonics you can take an ecosystem-level perspective, reasoning in terms of aggregate metabolic function rather than single strains.

This recent shift is largely why we’re seeing the an explosion of interesting research in this area.

Your microbiome is strongly correlated with your happiness, stress levels, nutrient intake, and immune system function. If we’re going to figure out what “optimal food” is, we must consider our gut flora.

Right now the soylent community is IMO doing a great job at nutrition, but is basically ignoring the microbiome. It’s being left to chance. I’m seeing reports of diahrrhea[1], and abnormal/unstudied microbial compositons[2], which are not good signs.

(edit: new users can only put two links in a post, I will try posting my collection of links in the comments)


Today I’m tossing my hat in the ring by launching the first modern probiotic.

It’s the first probiotic designed by reasoning directly about ecosystem-level metabolic function, and consequently the first to provide ecosystem-level fixes. This difference leads to a more robust solution than can be found using narrow-purpose strains, and is what I mean when I call it the first modern probiotic.

The product is non-prescription, as the best product I currently know how to create basically moves your bacterial intake towards those of your ancestors. We strongly considered naming the product PaleoBiotics, but decided this might accidentally make it a niche product.

We’ve been testing our product in a closed-beta for the last 45 days. Effects so far seem to be centered around 3 effects:

  • Increased mental and physical energy. Likely cause is simply better digestion.

  • Decreased stress levels. Jury is still out on cause, but this agrees with the papers currently making headlines about correlates between gut microbiome and mood.

  • Smellier turds… which I’ll go ahead and say is from better digestion :stuck_out_tongue:

Want to learn more?

Our product page is http://www.generalbiotics.com/probiotics

If you’re interested in learning more about your microbiome, Coursera is running a Human Microbiome class at
https://www.coursera.org/course/microbiome, we have a science section at generalbiotics.com/probiotics, and if you ask quetions here I can get my co-founder to answer them (his disertation was on the metagenomics of these systems, and he did his postdoc with the NIH’s Human Microbiome Project).

Do you want to help? Get the word out!

Know a reporter? This story might interest them.
Run a blog? Perhaps this would make a fun blog post.
Have a HN/Reddit account? We’re posting there soon, upvote us if you see us :slight_smile:

Thanks for being awesome!

Cheers,
David


#2

Sadly, as a new user, I still can’t post references more than two references at a time.

For [1], google for “soylent diarrhea” – I have a collection of reports I thought were particularly interesting, but I suppose those aren’t so important to post.

[2] http://aeon.co/magazine/health/would-we-opt-out-of-food-if-given-the-chance/


#3

If it makes turds smellier, it must make gas smellier too. I’m going to have to pass on this.

I’ve been taking the Safeway brand probiotics (It’s called 10X, or something like that) for several months now and I’m quite happy with it. It has a strain similar to the one in Align, along with a bunch of other strains.


#4

Our forum has talked about gut flora quite a few times.

:smiley: This sounds like a dangerous combination with Soylent haha

I will say that this is basically self advertisement on the Soylent forums, but I am going to let it slide personally :wink: since the topic is interesting.

Can you tell a little more about your product in terms of what is actually different… what bacteria are you adding to the system exactly and what are their functions? Are you sure they are doing their intended job? Do they actually synergies in our gut? (competing bacteria to my understanding isn’t optimal.) Are you sure there isn’t a product that isn’t better than yours?


#5

Good questions Tordenskjold. And I can’t see myself ingesting bacteria strains from a small, new company.


#6

:stuck_out_tongue: Unless ofc these bacteria are exactly the same as in other similar known products or that they been proven safe and “effective” by other valid sources


#7

I just looked at the website and your explanation for not revealing which strains the product contains comes across as strange and somewhat suspicious.


#8

I would give them the benefit of my doubt :slight_smile: I don’t think anything fraudy/dangerous is at play here. I am very interested in hearing about these 115 strains though.


#9

Thanks. We do also want to talk about the microbiome in general…

The probiotics in safeway basically follow 1907 designs of Élie Metchnikoff. They are based around the premise of single strains to do single jobs. Usually wheat digesting yeasts and milk digesting bacteria. Modern science biology doesn’t look at bacterial ecosystems this way – aggregate metabolic function is where it’s at.

And when you start looking at aggregate metabolic function, one of the more surprising findings is that western diets cause bacterial depletion. There is some debate on final cause here, but the sterility of modern diets seems to be a big cause.

Our current design is represented well by the product page. We are attempting to provide the symbiotic microbes who are unintended victims of modern food sterilization techniques.

This is the reason our strain count is higher – we are not trying to add something to digest a specific food, we want to provide a minimal general ecosystem for digesting all foods.

Intended function advertising is therefore in aggregate :stuck_out_tongue:

Fair enough. I want to stress that all the bacteria in Equilibrium are food safe, and I hope the website did a good job explaining my co-founder’s and my backgrounds in this area (Beltran specifically has been doing metagenomics for 10 years now). I can understand this perspective though.

We were hoping Soylent users would be interested in new approaches :stuck_out_tongue:


#10

I’d like to see what strains where included and the reasoning behind their inclusion. According to your F.A.Q. your working on this.

Why is it difficult? Current microbiome research does not think in terms
of species or strains, it thinks in terms of metabolic function and
OTUs (operational taxonomic units). This is because two microbes that
belong to the same “species” can perform very different functions in
your gut. Same name, very different behavior.

(from http://www.generalbiotics.com/faq )

When it comes to same species, don’t they have some way to identify the specific strain or behavior?

I’d say competing itself is optimal (helps keep microbes in check), its when one species or strain out competes the others is when it is no longer optimal (you lose the functions the other species/strains where preforming, and it gets harder for the immune system to keep this now out of control strain in check).


#11

It should be mentioned that Soylent did improve digestive issues a lot with 1.1, but for science I hope someone would be willing to try your mix of probiotics with Soylent :slight_smile: , I am sure many of the 115 strains wont be doing much to help digest Soylent, specially with the newly added enzymes… But who knows how many of them will :slight_smile:

I would personally be interrested in a list of the specific probiotics and their intended jobs. But I imagine you are keeping that tight in terms of competiton?


#12

I imagine there would be a survivial of the fittest between the probiotics in terms of who is most efficient at breaking down the food. The most efficient would get to multiply more in that ecosystem (thats a good thing) but that would also largely depend on what you are eating. This is when I think the large amount of different probiotics becomes good. Soylent isn’t really varied though, so a few of the probiotics would end up dominating your guts. (Not bad)


#13

I think this is right to some extent, though I’m less willing to say that low diversity gut microbiomes aren’t bad. Your flora do more than just break down your food.

For an example of what I’m worried about, it seems like gut diversity is lower right before an episode of Cdiff (http://www.microbiomejournal.com/content/1/1/18). Studies on the effects of the microbiome on stress and mood are being performed right now. We already know that there is communication between the microbiome and the enteric nervous system.

I think Soylent 10.0 will have ingredients specifically designed to keep our microbiomes diverse.


#14

I think it is very unfortunate that on the one hand you claim to have scientific research backing all this up and on the other hand you need a quack miranda warning for you whole site and product.

It’s probably better if you use the official text instead of the custom version you made: http://en.wikipedia.org/wiki/Quack_Miranda_warning

I for one would like to see a proper double blind randomized controlled trial where you measure the effects between people taking the product you made and a placebo, and maybe a control group taking nothing.

Finally what i gathered about smelly stool so far is that it actually means digestion is going wrong, so in that case the product would still need some tweaking to fix that.


#16

I’m in the same boat as @Tordenskjold, this is definitely self-promotion But the idea is interesting, and relevant to the community and its goals, I think.

@davidsalamon Will you eventually be revealing a list of the bacterial strains and their purpose? And just to confirm, this product is intended to be a one-size-fits all for all diets?

Other than that, I’m definitely interested in this concept. I don’t think I can invest money into this at the moment, but I’ll accept free samples. For science. And I’m curious how it interacts specifically with an exclusive near/exclusive Soylent diet.


#17

This was a very difficult thread to participate in. It marks the first time I’ve had quack anywhere near my name. Not a good feeling.

It took a while, but thankfully I’ve remembered that what separates a quack from a scientist isn’t the presence of absence of an FDA warning (basically a requirement for non-prescription science), it’s not even the presence or absence of credentials, publications, or expertise (all of which we have in spades here) – it’s the product.

So thank you for that. Better to learn the lesson here than down the line.

Yes. It’s not optimal for all diets, but it’s better than nothing. Our website has the full list of who we think should be cautious.

Cool! Are you in the Bay Area? I’ve had it on my list to get a ~100% soylent stool sample for a long time now. Perhaps we can trade a bottle for a sample?

edit: david@generalbiotics.com if you want to discuss off forum

edit 2: actually, if possible a before and after stool sample would be ideal.


#18

Hi davidsalomon,

I had no intention of calling you a quack, i’m sorry you had that feeling.
The reasons i stress the FDA warning are:

  1. If you prove your product does what you say it does in a proper clinical trial you don’t need the warning for your claims anymore.
  2. You altered the text and i have seen some cases of FDA shutting websites down for using a modified version of the text.

I have high hopes for products like these but my standards for evidence are pretty high.
Websites that promote this for me are:
http://www.sciencebasedmedicine.org
http://lesswrong.com/
and to a lesser extent: http://examine.com/


#19

This product interests me. In that Aeon interview where Rob was talking about how his gut microbes are much different than norm makes me wonder if an exclusively Soylent diet will kill off (or at least reduce population) of a lot of different types of microbes that aren’t useful in such a diet. And produce an abundance of microbes that do work the Soylent. If yes, perhaps some wouldn’t care, if they can continue exclusively with Soylent. If someone wanted to eat normal food from time to time however, it might be beneficial to have some of the other microbes. A product that provides a diverse collection of microbes could be a great companion product with Soylent.

That said, I’ve never studied the microbiome, don’t truly understand the purpose of the microbes, and have doubts as to whether I used the right words in the right places. It makes sense to me, I’d like to learn more, I’m not willing to buy right now. If someone like livingparadox gives it a good thorough test maybe I change my mind - no doubt we’d get excellent documentation of the experience, whether it’s good or bad.


#20

This post made me giggle like a 13 year old girl. That being said, I hope someone at least will take you up on that offer, perhaps since you are potentially analyzing soylent user stool samples anyway, you could then provide the community with insight to any findings you get from it? I am sure you could use multiple samples from more people in return for samples of your product? (Just the fact you asked for stool samples proves to me how serious you are about this product, kudos!)


#21

On forum, off forum, I’m not particularly concerned. I’ll send you an email though. I’m actually closer to OC (one county over). But I’m totally down with it. I’ll definitely document it for the community.