There is no 'healthy' microbiome
nytimes.com
There is no 'healthy' microbiome
1–10 of 17 posts
Re: There is no 'healthy' microbiome
#2The 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 hacking based on the fact that the experimenter does't have c. difficile. Does the author really believe that c. difficile, or other acute health problems, are the only possible results of an unhealthy microbiome?
It seems most plausible that dietary health is going to be a function health(microbiome, diet/environment, genetics). I doubt anyone thinks it will be a simple function, but along with acutely unhealthy microbiomes, there will be some obvious (given enough long-term data) problematic microbiomes across wide genetic and dietary variations, that don't quickly cause acute disease. And I don't think there will be as much variation as the author believes in healthy microbiomes once you start controlling for genetics and diets.
Re: There is no 'healthy' microbiome
#3The 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…
I take this article to be an argument against snake-oil panaceas, just broadly overstated in its phrasing. Not a generally useful piece, but a healthy rebuttal to the woo reductionists.
Re: There is no 'healthy' microbiome
#4Bonus points for the quote This befuddling complexity is not confined to the vagina.
Re: There is no 'healthy' microbiome
#5The 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 balance a little too much one way or another can potentially cause symptoms of Autism Spectrum Disorder. There are at least two startups in stealthmode that I know of that are pushing microbiome matching between "healthy" donors and "unhealthy" recipients -- very much like snake oil salesmen. One person's healthy is another's unhealthy but these groups and their VCs apparently don't give a shit (VC funding in science is a while other can of worms).
If you want to be a microbiome hacker, go contribute YOUR microbiome to publicly funded by you research. I suggest the American Gut Project[1][2] for people in the US and British Gut[3] for those in the UK and EU. For $99 you can learn about your microbiome and contribute to largest, most successful crowdfunded research in the world. This project is entirely supported by people like you and me, directly.
[1] http://humanfoodproject.com/americangut/
Re: There is no 'healthy' microbiome
#6The 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…
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 makes me wonder if the species % data presented by ubiome is presented with false precision.
Re: There is no 'healthy' microbiome
#7Earlier 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…
µBiome is vapid consumerism in my opinion. They don't contribute data to the research community (as far as I know).
The vast, vast majority of all bacteria are not culturable in a lab. That being said, we use rRNA/rDNA sequencing[1] to build phylogenies based off of BLAST E-values[2], or how likely it is two sequences evolved separately from each other. We have cultured and sequenced enough of the big three (and many of the top 100 gut microbes) that we can be statistically sure that they're related. We can't say for sure two different but closely related sequences are two different, closely related species but we can say they're related OTUs[3]
[1] http://greengenes.lbl.gov/cgi-bin/nph-index.cgi
[2] http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYP...
Re: There is no 'healthy' microbiome
#8The article gives a lot of neat background, but primarily
deconstructs a straw man argument.
He does a pretty good job of presenting the actual argument for microbiome experimentation at the end:
>our genomes have had little time to adapt to modern life, but our microbiomes have had plenty.
>It may be that a Hadza microbiome would work equally well in an American gut, but incompatibilities are also possible. The conquistadors proved as much. As they colonized South America, they brought with them European strains of Helicobacter pylori, a stomach bacterium that infrequently causes ulcers and stomach cancer, and these European strains also displaced native American ones. This legacy persists in Colombia, where some communities face a 25-fold higher risk of stomach cancer, most likely due to mismatches between their ancestral genomes and their H. pylori strains.
Re: There is no 'healthy' microbiome
#9The linked author doesn't seem to have a clear thesis statement, but from the examples given (the Hadza and the Conquistadors) it appears the thesis statement could be something like this: "Each isolated ancient human community already has basically optimized microbiomes. In each such human niche, their traditional microbes can probably survive in that niche. Also, those same microbes will have been surviving for so long that second order optimizations (like ethnic genetic adaptation to the potentially harmful parts of their traditional microbiome package) have likely occurred. In the face of such 'bio-traditions', and their presumptively functional state, we should tread carefully, and study everything before we muck about too much."
This seems to me like an excellent argument for why people who grew up on family farms, or in jungles, or other vaguely historical places should not muck about too much with their microbiomes. Heck, even third generation New Yorkers are probably solid.
However, it seems to miss the point that urbanization, immigration, antibiotic use, and radically weird diets (to name a few factors) are happening all over the modern world.
Given the modern situation, having already been disrupted by biologically unprecedented events for centuries, it seems plausible that at least some of us are like sailors at sea, with the metaphorical equivalent of scurvy-before-its-etiology-was-determined.
Just as, if you have scurvy, it doesn't cost much to try eating citrus and see if it helps, it seems that for people who are already unhappy with their gut health, it probably doesn't cost much to experiment here.
If you can already see that your digestion/mood/hunger is funky by comparing it do to friends and family, and you can read the research on that suggests these processes can be affected by microbiomes, it seems plausible to me that checking out uBiome or General Biotics or one of the "dating websites for poop" (or whatever, I'm sure there are more of these things floating around) it doesn't seem that crazy to me. A bit crazy, yes. But way less crazy than the same experimentation would be for someone who is eating and living in the same manner as their mother's mother, and has no more tummy troubles than any of their grandparents.
I've published a little in this area, and I didn't know about the conquistador story, so the article was appreciated, but I'm also personally a fan of experimentation that is early, fast, and cheap and I didn't see any of the experimental cost benefit analysis that could have been there, and could have made the article better.
Re: There is no 'healthy' microbiome
#10This 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 the microbiome equivalent of the paleo diet -- it simply restores non-pathogenic microbes which were the unintended victims of widespread food sterilization. In our (admittedly small) pilot study, over 90% of people felt this helped their digestion.
I believe this approach is more cautious than continuing to eat a modern diet. We didn't evolve eating sterile food.