3 ms·

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

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 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.

sunspeck 12y ago
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.
aroch 12y ago
>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/ http://humanfoodproject.com/americangut/ [2] https://fundrazr.com/campaigns/4Tqx5 https://fundrazr.com/campaigns/4Tqx5 [3] https://fundrazr.com/campaigns/4sSf3/ab/5qJ7f https://fundrazr.com/campaigns/4sSf3/ab/5qJ7f
- krrrh 12y ago
  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.
  - aroch 12y ago
    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 http://greengenes.lbl.gov/cgi-bin/nph-index.cgi [2] http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYP... [3] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609233/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609233/
  - derekja 12y ago
    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.)
- dlss 12y ago
  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.

sunspeck 12y ago

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.

aroch 12y ago

>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/ http://humanfoodproject.com/americangut/ [2] https://fundrazr.com/campaigns/4Tqx5 https://fundrazr.com/campaigns/4Tqx5 [3] https://fundrazr.com/campaigns/4sSf3/ab/5qJ7f https://fundrazr.com/campaigns/4sSf3/ab/5qJ7f

krrrh 12y ago
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.
- aroch 12y ago
  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 http://greengenes.lbl.gov/cgi-bin/nph-index.cgi [2] http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYP... [3] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609233/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609233/
- derekja 12y ago
  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.)
dlss 12y ago
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.