Gut microbiome tells your health

Hi Quantified Selfers,

I’m Yosuke and microbiology & immunology researcher at UCSF.
My colleagues and I plan to launch startup company to provide gut microbiome data which means “all species information about gut bacteria”.
We can tell the abundance of lean/obese related bacteria and high cholesterol related bacteria in your gut.
You just simply send stool sample to us weekly/monthly. No blood collection required.
Is it interesting to you?
Let me know your question, opinion, advise, request and suggestion for price, service and whatever about microbiome:shy:.


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Hi Yosuke - I think this is an interesting area, but I suspect you would get better comment from the QS folks, who generally are pretty well informed, if you provided more detail about what you were doing so people could ask specific questions. For instance, what is the taxonomic distinction you are using between lean/obese related bacteria? Are you characterizing gut microbiome data by genotyping? Culturing? Or something else? The more details you can share about what you are doing, the more likely you will be to get good feedback.

Hi Gary,
This is Shoko - working together with Yosuke. We are still at very early stage and wondering what kind of information is useful for people. We are basically thinking DNA based sequencing or just PCR to detect overall or specific taxa of interest. If more people are interested in obese/lean type, we could provide Bacteroidetes/Firmicutes ratio (gross index), quantity of Akkermansia (negatively correlates to obesity and type 2 diabetes; detailed index) for example, and/or overall changes compared to known obese/lean types (principal coordinates analysis; visually indicates overall changes). There are many other bacteria known to be associated with high-cholesterol, inflammation, etc. We would like to know which variable would be of interest, how often, how detail, how much (cost) it would worth, etc. Let us know any thoughts you have, happy to answer any questions!

I think there is tremendous uncertainty among even advanced users of QS methods about how to think about this topic. It would be great to explore with you. One way of getting excellent feedback would be to organize a gut microbiome tutorial. This would be sure to attract some interest. The questions I recommend discussing are:

What taxa are of most interest based on state of research knowledge today?
How can these be identified; what are the metrics of interest?
Examples of cases where tracking microbiome led to useful results.

If one or both of you can come to the Amsterdam conference next May, I would gladly add this to the program. Perhaps we could do some experimenting together beforehand, and use the results as a basis for the discussion there.

Thank you for your suggestion, Gary.

Recent studies showed that several species of Clostridium are increased in obesity/Type2 diabetes, while Ruseburia is enriched in normal people.
We would provide information about these “key bacteria” but not entire microbiome by using quantitative PCR which could be way cheaper than meta-genomic analysis by next generation sequencer.
It seems like some metabolites derived from these bacteria could directly cause obesity, meaning that the dramatic change in our lifystyle won’t make sense unless it also changes gut bacteria constituents. In the other words, slight change in your lifestyle might be enough to adjust your gut bacteria balances (nobody knows perfect answers yet). This is just my assumption but I believe it is worth to monitor constantly (maybe once or twice a month).

We recently came up with this idea, so we need experiment as you mentioned. But before moving forward, we want to make sure people who want to use this method are not only us. Please wait and see if we can go on this track.


This is very interesting.
Your message would also be relevant in the categories ‘Health’ and/or ‘Diet, nutrition & weight’ of this forum…

A few questions:

  • You told about correlation with obesity and diabetes, but are there correlations with (and thus benefits to do this for people with) other health conditions too?

  • Specifically, has there been research done on the gut genome of people with Irritable (not: Inflammatory) Bowel Disease?

  • Is it possible to influence gut flora with diet or anything else? Do you give information about this with the results? If the outcome is “you have flora that greatly increase your chance of …”; is it accompanied by info about how to change the gut microbes to decrease this risk/presence?

  • [quote] send stool sample to us weekly/monthly[/quote] So repeated samples are needed? How long/how many stool samples would it take to complete the sequencing?

  • How much does a full seqencing of one’s gut genome cost?

  • Does your company cater only to people living in the US, or worldwide? Is it a problem if stool samples would take longer to be sent to your lab, if from further away places?

Best regards,

Hi Lisa,

Thank you for posting.


  • You told about correlation with obesity and diabetes, but are there correlations with (and thus benefits to do this for people with) other health conditions too?
  • Specifically, has there been research done on the gut genome of people with Irritable (not: Inflammatory) Bowel Disease?[/quote]
    Yes, gut microbiome is very different between healthy and either IBS or IBD people.
    Interestingly, several studies reported the dramatical change of gut microbiome in autism people.
    In addition, aging, hypercholesterolemia and certain types of cancers.

Great question. Currently, many researchers are trying to clarify whether altered gut flora is causality or consequence of disease (or both). Furthermore, we cannot provide diagnostics. We cannot say “you are T2DM”. Instead, we have to say “your gut microbiome is more like T2DM patients”. As 23&me provoked a lot of issues, FDA seems making new rules. Besides that issue, there are three major methods to modulate gut flora; diet, antibiotics and probiotics. In terms of diet, we can recommend better one without sequencing; just reduce oil and carbohydrate increase vegetables, that’s it. Use of antibiotics cause a lot of troubles (i.e. C. difficile super infection), we will never recommend. Probiotics would be the best choice to control gut microbiome, however very few evidences support the effect of currently available bacteria strain contained in commercial probiotics; Lactobacillus and Bifidobacteria.
Rather than using these bacteria, we plan to provide the bacteria you lack based on the sequencing data. Again, causality is still under arguing, however, I believe adding back bacteria you don’t have would be more rational than taking bacteria that cannot inhabit in your gut.

Less than 1 gram of stool is enough for sequencing. It will take a week to complete sequencing and analysis. Frequency of sampling is dependent on how often people want to quantify themselves. Ideally, sequence once, we compose personalized probiotics based on that result, you may try this for 1-3 months, and then sequence again to make sure that probiotics really works.

It will cost $80-120 to read gut microbiome by next generation sequencer. In case of reading 10-15 of marker bacteria for each disease, it will be $20-40.

Initially US only.
We can expand our business because stool sample is stable inside denaturing buffer. As long as Fedex can reach, we will send a kit and receive sample. But providing probiotics would be very difficult due to the regulation. Even inside US, we need to register new bacteria for probiotics to FDA before composing probiotics.

Hope these help you.
LEt me know if you have further questions.


Thank you for your quick reply, that clarifies a lot.

Especially about the multiple samples; I misread your original post as meaning ‘sequencing has to be done multiple times before it can be completed’, but you meant it more as ‘follow-up’ - that makes a lot of sense.

Regarding the autism correlation, that is very interesting; it is known autism is correlated with gut symptoms in general, and specifically with both Irritable Bowel Disease and Celiac Disease. The correlation with the gut flora on top of that, makes this link even stronger. But I guess not a lot is known yet about what is the cause and what is the effect here (is that right?)…

I have to say the price for the sequencing is much more affordable than I would have thought! I wonder how many people in the general public would be interested to do this; but since the price would be affordable for the general public I guess many people would consider this.

I would be interested to do this; since I am not in the US your lab wouldn’t be an option (it’s good you clarified that, BTW - this forum is read internationally), but I wonder if there are labs in Europe doing this?

Best regards, Lisa