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Meet Your Microbes: uBiome Offers New Service

We are not alone. Walt Whitman didn’t know how right he was when he said, “I contain multitudes.” The microbes on and in our bodies outnumber our own cells 10:1.  Perhaps that creeps you out. Perhaps that makes you curious to know just who all these billions of creatures are that are using your body for a home and a transportation device.

For just $89 you can learn what’s in your gut, nose, mouth, skin, genitals…or sample anything!

The offer comes from uBiome, a “citizen science startup” that has scientific goals somewhere down the line, but for the moment is happy to just provide a personal service, to sequence your microbiome and tell you how you compare to others. The current utility of this offering is questionable. It’s just not ready for prime time.

You are urged to become a “citizen scientist” by contributing your microbiome information to a huge database of other contributors. You get a sample kit, swipe a sample swab across the appropriate area, and mail it back to them. You also fill out an online survey that asks questions about your health, lifestyle, demographics, social connections, and more. You can see how you compare to others, and eventually the data may be used to explore questions about the influence of the microbiome on health.

The choices

  1. For $89 you can choose to sample your mouth, nose, genitals, or gut.
  2. For $159 you can sample your mouth and gut.
  3. For $399 you can sample all 4 of these sites, plus a 5th site behind the ear.

These tests provide a snapshot at one point in time. Your microbial flora will change over time, providing a reason to repeat testing and continue to generate income for the company.

For $229 you can sample your gut bacteria 3 different times, perhaps to gauge the effect of antibiotics or the response to probiotics or changes in diet.

The process

It would be too expensive to do full sequencing. What they are doing is called 16S sequencing, measuring a ribosomal gene in bacterial DNA. They are able to filter out genetic material from humans and other organisms and classify bacteria at the genus level. 16S sequencing is an accepted method of identifying bacteria, but it is problematic. The sequences in some databases are inaccurate, there is no consensus quantitative definition of genus or species, and microheterogeneity within a species is common. False positives occur. In some cases no identification is possible; 14% of bacteria can only be identified by genus. And that can make a BIG difference. Streptococcus is a genus that includes various species, some of which are harmless skin flora, one of which causes strep throat and scarlet fever, and one of which (Strep. pneumoniae) is the target of an immunization, the pneumonia vaccine. Staphylococcus can be the harmless skin dweller Staphylococcus epidermidis or the killer methicillin-resistant Staphylococcus aureus (MRSA). If I were carrying MRSA, I’d like to know about it, but telling me I have bacteria of the genus Staphylococcus would be meaningless, since we all carry some species of that genus.

16S testing can only hope to identify bacteria that carry those ribosomal genes. It can’t identify other microbes we carry, like Archaea, yeast, fungi, and protists.

IRB approval

The website says they have received Institutional Review Board approval to perform research studies. Customers who want to participate will sign a consent form. No consent form is required for the basic service of microbiome compositional analysis and interpretation for private individuals.

“Ethical shenanigans”?

Blogger Melissa Bates is worried about what she calls “ethical shenanigans.” Her concerns:

  1. Participation requires the payment of a fee
  2. There is no clear statement about what will be done with the data or samples.
  3. There is no apparent plan for how your identity will be protected.
  4. It’s not clear what conflicts the major players in the project might have.
  5. The benefits you’ll receive are grossly over-stated. They do state that it is not a diagnostic test, but they recommend discussing results with your doctor and say the information may be useful in treating difficult disease.
  6. There’s no statement as to what your risks of participation are.
  7. Children are included, but it’s not apparent how they are protected.

After responses from the company and other bloggers, Bates wrote some final thoughts:

We can now safely say based on statements left here and at Comradde Physioprof’s blog that uBiome has not received IRB approval for their project, despite having made what I believe to be grossly over-stated claims about the applicability of their data to human disease and the fact that they have already collected money from their subjects and are in possession of potentially identifying data from their future subjects.  That makes this “ethical shenanigans.” I believe that this is made more egregious by the fact that they used their university affiliations to “sell” their donors/subjects on the fact that they could complete their study as they described.

What do we know about the microbiome?

We have just begun to dip our toes into this unexplored ocean. We have learned that certain gut bacteria may be related to obesity and that Clostridium difficile infections can be successfully treated with fecal transplants. It has been speculated that bacteria might be implicated in diseases like autism, depression, multiple sclerosis, etc. A company official told The Guardian:

 We are doing exploratory science, and hope to discover correlations that will be useful in understanding health and disease, new bacteria that have not been previously studied, and other knowledge.

The Human Microbiome Project at the NIH, characterized as a feasibility study, is attempting to establish a database by more systematic, conventional scientific methods.

Problems with this kind of research

  • It’s unsystematic.
  • Only those who have the money and interest will be tested; this will not be a random sample of the population and could skew results in unforeseen ways.
  • One-time sampling is not representative of the individual’s life history; it could easily miss microbes present earlier in time that triggered a given disease, or it could identify microbes that were only present transiently and were insignificant.
  • It’s the mother of all fishing expeditions. They are bound to find correlations galore just because of the mass of data, but correlation is not causation. Further studies will be required to tease out meaningful data from the noise and look for evidence of causation.
  • It is inevitable that false conclusions will be drawn prematurely.
  • It will raise a lot of new questions, which is a good thing; but it can’t provide any answers.

Problems with individual testing

We don’t know what constitutes a desirable microbiome. Efforts to increase the population of one microbe might benefit you in one way while harming you in another. We don’t begin to understand all the permutations and the ways in which bacteria influence each other. It’s an incredibly complex ecosystem, a web where tweaking on one part might drastically warp other parts. You can test your microbiome before and after starting a diet, and you may see some changes; but how will you interpret what the changes mean? You won’t know whether the changes were due to your diet or to some other factor.

Comparison with genome testing

Personal genome testing is being offered to the general population by numerous companies. It doesn’t sequence the entire genome, but only SNPs (single nucleotide polymorphisms). The company 23andMe advertises that on average, one person in five develops diabetes by age 79, and that variations in your DNA that they test for might raise your risk to one in three. That’s not particularly helpful. Diabetes is multifactorial. Genes are not destiny. Having the associated genes doesn’t mean those genes will be expressed, and it doesn’t tell us how other genes or environmental factors might affect gene expression. Even if you are only at average risk, you ought to already be making appropriate lifestyle choices like exercise and weight control; you shouldn’t need whatever additional motivation the knowledge of a slightly higher risk might provide.  They test for a rare mutation that is associated with a nearly 60% lifetime risk of Parkinson’s disease, but if you have that mutation there is nothing you can do to reduce your risk, and there is a 40% chance you won’t get the disease anyway. BRCA1 is a highly significant mutation, with a risk of breast cancer as high as 87%, and we have an effective way to reduce that risk. That was the reason Angelina Jolie decided to have both breasts removed. If she had relied on direct-to-consumer genomic testing, they wouldn’t have detected that risk: because of patent protection, there is only one company that can test for BRCA1.

Direct-to-consumer genomic testing promises much but delivers little. It isn’t good for much. uBiome is good for even less.

Conclusion

As a scientific endeavor, uBiome is questionable. As a personal medical test, it is essentially meaningless at our current state of knowledge. Just because we can test something doesn’t mean we should, and it doesn’t mean we will be able to understand the test results, much less do anything about them to improve our health. Biome testing is simply TMI (too much information).

Posted in: Diagnostic tests & procedures, Medical Ethics

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