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There is no 'healthy' microbiome

nytimes.com

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Re: There is no 'healthy' microbiome

#11

Post by dlss »

aroch wrote: post #5
harshreality wrote: post #2

The author seems to get carried away, emphasizing that microbiomes (measured by host health) do not form a totally ordered set. I think that's a caricature of what microbiome hackers are claiming. A totally ordered set would mean there's one "best" microbiome. But there might be one or only a few "best" microbiomes for a particular person with a particular diet. In one section, the author criticizes microbiome hackin…

>microbiome hackers I really wish this wasn't a thing. I'm getting tired of all the "startups" in my field (microbio) who are pushing microbiome-based treatments. They're not currently regulated by the FDA and they are downright dangerous. The healthy gut is primarily made up of (~90%) Firmicutes, Bacteroidetes, and Clostridium of which the majority are uncultured, unsequenced and completely unstudied. Shifting the b…

So I can't speak to the specifics of the startups you're referring to (I don't know who they are), but I will say I'm very surprised to have read this.

The responsible development of new therapies is almost always a good thing. I'm confused to hear you say they're not FDA regulated, since the FDA is very clear: if it's intended to treat a disease, it's regulated. Perhaps you could explain what I'm missing?

Also technical note: these microbes are not unknown/uncultured/unsequenced. See MetaHIT, the Human Microbiome Project and the American Gut Project you mentioned.

Re: There is no 'healthy' microbiome

#12

Post by johnvschmitt »

If you brush before sleep (with triclosan, a very common antibacterial agent), you breathe >25% of your breaths through a mouth populated with antibacterial agents.

The prevalence of antibacterial agents in soaps, & toothpastes in the last 15 years coincides with the increases in asthma & digestive disorders.

The article says, essentially, "It's complex, and adaptive, so be careful how you force it away from a neutral state." Yet, adding antibacterial agents to toothpastes is quite a forceful change.

Re: There is no 'healthy' microbiome

#13

Post by aroch »

dlss wrote: post #11
aroch wrote: post #5

Earlier quoted context omitted.

>microbiome hackers I really wish this wasn't a thing. I'm getting tired of all the "startups" in my field (microbio) who are pushing microbiome-based treatments. They're not currently regulated by the FDA and they are downright dangerous. The healthy gut is primarily made up of (~90%) Firmicutes, Bacteroidetes, and Clostridium of which the majority are uncultured, unsequenced and completely unstudied. Shifting the b…

So I can't speak to the specifics of the startups you're referring to (I don't know who they are), but I will say I'm very surprised to have read this. The responsible development of new therapies is almost always a good thing. I'm confused to hear you say they're not FDA regulated, since the FDA is very clear: if it's intended to treat a disease, it's regulated. Perhaps you could explain what I'm missing? Also techn…

They're not marketed to cure a disease, they are "probiotics". They are using the yogurt rule

>Also technical note: these microbes are not unknown/uncultured/unsequenced. See MetaHIT, the Human Microbiome Project and the American Gut Project you mentioned.

Yes the are, we have metagenomics on them (v4 rDNA sequence reads) not full seq data. We can't ID which bug and then grow it. We just know some of its rDNA is in the mix. Being able to phylotype =/= known microbe.

Re: There is no 'healthy' microbiome

#14

Post by derekja »

krrrh wrote: post #6
aroch wrote: post #5

Earlier quoted context omitted.

>microbiome hackers I really wish this wasn't a thing. I'm getting tired of all the "startups" in my field (microbio) who are pushing microbiome-based treatments. They're not currently regulated by the FDA and they are downright dangerous. The healthy gut is primarily made up of (~90%) Firmicutes, Bacteroidetes, and Clostridium of which the majority are uncultured, unsequenced and completely unstudied. Shifting the b…

How do you think ubiome.com compares with these efforts? I did an analysis with them and feel like I got some insights, but I also felt that the way the data Is currently presented could lead to a lot of false conclusions, especially for people without a microbiology or statistical background. I'm also curious about your statement about how many strains are unsewurnced and unstudied. I've read this elsewhere, and it…

I quite liked that it was possible to download my raw data file from ubiome. I got my first results back a couple months ago. Then I got sick and in a while I'll know precisely how a course of antibiotics devastated my microbiome (but killed what it needed to, so I'll probably live.)

Re: There is no 'healthy' microbiome

#15

Post by 001sky »

dlss wrote: post #10

This article doesn't seem to consider the alternative hypothesis very seriously, so as one of the biohackers Ed is no doubt referring to, I'll do my best to summarize why it's not unreasonable to act before all the data is in. Our knowledge about the microbiome is similar to our knowledge of nutrition: we don't know enough to claim optimality, but we do know enough to say that the modern default is bad. My product is…

"we do know enough to say that the modern default is bad."

Could you articulate why this statement is even plausible?

Re: There is no 'healthy' microbiome

#16

Post by dlss »

001sky wrote: post #15
dlss wrote: post #10

This article doesn't seem to consider the alternative hypothesis very seriously, so as one of the biohackers Ed is no doubt referring to, I'll do my best to summarize why it's not unreasonable to act before all the data is in. Our knowledge about the microbiome is similar to our knowledge of nutrition: we don't know enough to claim optimality, but we do know enough to say that the modern default is bad. My product is…

"we do know enough to say that the modern default is bad." Could you articulate why this statement is even plausible?

Interesting. To be clear, the current state of affairs is eating sterilized food (often required by law to control pathogens), and taking antibiotics every 2 years[1].

This is bad a priori, since it's two deviations from the only known good condition -- the one we evolved in.

But I take it that argument was non-persuasive.

So here are some other people discussing the idea: The hygiene hypothesis[2] is broadly the theory that diseases of affluence[3] are related to living in overly sterilized conditions. Most if not all of the items discussed in [3] are correlated with your microbiome[4], with large studies underway to determine the role in more detail [5].

Okay, hope this helps. To answer your question a third way: most biologists working on the microbiome think it's plausible.

[1] http://www.nejm.org/doi/full/10.1056/NEJMc1212055

[2] http://en.wikipedia.org/wiki/Hygiene_hypothesis

[3] http://en.wikipedia.org/wiki/Diseases_of_affluence

[4] http://academy.asm.org/images/stories/documents/FAQ_Human_Mi... -- see pages 11+

[5] We have a bibliography at http://www.generalbiotics.com/science

edit: my co-founder wishes me to point out that I wrote this was to illustrate why eating ancestrally normal microbes is a plausible idea. Please don't take these links as me saying my product can prevent any diseases -- I don't have sufficient evidence to support that claim.

Re: There is no 'healthy' microbiome

#17

Post by dlss »

aroch wrote: post #13
dlss wrote: post #11

Earlier quoted context omitted.

So I can't speak to the specifics of the startups you're referring to (I don't know who they are), but I will say I'm very surprised to have read this. The responsible development of new therapies is almost always a good thing. I'm confused to hear you say they're not FDA regulated, since the FDA is very clear: if it's intended to treat a disease, it's regulated. Perhaps you could explain what I'm missing? Also techn…

They're not marketed to cure a disease, they are "probiotics". They are using the yogurt rule >Also technical note: these microbes are not unknown/uncultured/unsequenced. See MetaHIT, the Human Microbiome Project and the American Gut Project you mentioned. Yes the are, we have metagenomics on them (v4 rDNA sequence reads) not full seq data. We can't ID which bug and then grow it. We just know some of its rDNA is in t…

> They are using the yogurt rule

Ahh, you mentioned Autism spectrum, so I assumed that couldn't be the case.

> we have metagenomics on them (v4 rDNA sequence reads) not full seq data

There is plenty of genomic data beyond 16S. For the HMP, full sequencing of selected strains as well as hundreds of WGS metagenomes were done. And that's almost old news now, I'm sure there is even more being done currently. The result is basically either a full genome, or a set of giant chunks of the genome of the abundant microbes there. We don’t have all the genomes closed (although some are in the process!) but closing a genome is a very high bar and probably not worth it when you can get a lot of data from a fairly good set of large contigs.

Can the assemblies be chimeric/wrong/whatever? sure, some of them will be, but at this point most assemblies are fairly good :)

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