Screenshot excerpts showing Miss Vegan’s and Q Bob’s  Viome microbiome test results

A growing list of direct-to-consumer (DTC) microbiome genetic testing services have popped up in recent years since I first tested my own microbiome sample and wrote an article in Omicshelpdesk.com about it. If you are not familiar with the microbiome or with microbiome sequencing you might want to read that article first.  Since then, hundreds of millions of dollars in financing have been invested in microbiome testing startup companies like uBiome, Viome, Finch Therapeutics, Kallyope, Second Genome, Human Longevity, Maat Pharma, Seed.

Many of these startups are focused on nutrition and making diet recommendations as that is the most obvious application when studying gut bacteria which are in fact responsible for metabolizing the food we eat, and it is also the least risky business one may attempt at this still early stage of microbiome research. They all seem to have very nice reports and user interfaces from the screenshots I looked at. The one service I looked at more attentively this time around is Viome, by accessing the reports that a vegan friend allowed me to see in the Viome web site and app, which contained the results of her microbiome test. In this article I compare her results to those of a man who runs a personal blog called Quantified Bob. In his blog, Q Bob, as I will call him here, shares his experiences quantifying everything that can be measured in his body or about him.

But before presenting that comparison, I would like to bring some attention to two important inquiries we need to pursue before choosing and paying for a DTC microbiome test in order to assess its validity: (1) We should research if the technologies and methods the company uses have been validated; and (2) We should ask if the service offers access to the raw sequence data.

With regards to the first point, we should be aware that a month ago, uBiome was raided by the FBI and temporarily suspended clinical operations. Two testing kits that they sell through practitioners were cancelled, SmartGut a kit to analyze fecal samples, and SmartJane, a kit for women to analyze their vaginal microbiome. The company noted that it would continue to sell its direct-to-consumer product, Explorer. It is important to note that the reason the FBI got involved was linked to incorrect billing of insurance companies, and not the quality of the test. But how would a regular citizen go about investigating the quality of a test? Here are a few options: It would require researching the number and quality of peer-reviewed publications by that company which is accessible from Pubmed. It would require looking for and reading the main publications and patents that describe their technologies and data analysis methods. It would also require investigating which research institutes and public health agencies have used their services. uBiome has published a Code of Standards and Business Ethics dated May 2019 and it may be advisable to read those types of documents and the FAQ pages of any of the providers of DTC tests. Of course, most people do not have the time or the knowledge to read and understand those documents, but they have some options. They can look for forum discussions, although I have not seen any up-to-date ones, or they can look for review articles posted in a trusted media outlet in the Internet. At Omicshelpdesk.com, we will be activating our forums to do exactly that, offer regular people the ability to discuss with scientists, the different options for DTC omics tests.

With regards to the second point, it needs to be clarified that what is meant by “raw sequence data” are the bacterial gene sequences or transcripts generated by DNA or RNA sequencing machines that are processed and analyzed to create the report. If anyone has the expertise to analyze sequence data, such as a bioinformatician, then availability of the raw data gives the results more credibility as it can be used to validate the results. Even if you cannot analyze the raw data, you can hire someone who can help you with that, such as the data analysts at Omicshelpdesk.com. Some companies make the raw sequence data available, such a uBiome, and some don’t, such as Viome. uBiome goes even further by not only providing access to the raw data but by describing how to analyze it, which is good because it gives a customer reassurance that the company does not fear that someone double-checks their results. And there are forums, like the Qiime forum, where someone with data analysis skills can get help in analyzing the uBiome raw data. Viome on the other hand, writes in their FAQ page, as an answer to the question “What is raw data and will I receive it with my results?” what I will summarize as “raw data is too hard for you to understand so we just give you the reports”. That is not a good policy but unfortunately HIPAA laws which apply to medical records and give a patient the right to access them do not apply to DTC genetic tests.

Let’s investigate now how Miss Vegan and Q Bob’s microbiome diet recommendations as reported by Viome compare to each other. Miss Vegan filled out a questionnaire in which by her answers she made it clear she is a vegan or vegetarian, therefore, as shown in the table below, her superfood recommendations are all plant-based, while Q Bob was recommended bone broth as a superfood. In her list of non-superfood protein recommendations (not shown in the table), Miss Vegan’s had eggs and milk products but no meats. This is not the case with Q Bob, who had grass-fed beef and lamb in his non-superfood protein list.

Viome provides a list of foods to avoid, as shown in the table below. In both cases, they had bell peppers in common in this list, the reason being that their microbiome contained “pepper mild mottle virus”, which is known to cause disease in bell pepper. And “Since plant viruses in the microbiome could potentially cause inflammatory symptoms in humans, it is recommended you avoid bell pepper.” For other foods, the bacteria or virus was not named, and the explanation was: “An analysis of your data indicates that avoiding XYZ will be beneficial for you” (replace XYZ with name of food to avoid, Miss Vegan got lentils in her “avoid” list). Also to note, in Miss Vegan’s sample they found a probiotic microbe Enterococcus faecium, but none in Q Bo’s sample.

The charts in the Microbiome Results section show that Miss Vegan and Q Bob have similar charts for Metabolic Fitness and Microbial Richness, but the inflammatory activity charts are very distinct between the two showing very low inflammation for Miss Vegan. Microbial inflammation processes take place in a person’s microbiome and are known to be associated with inflammation. It is known that shifting towards a more vegetarian or plant-based diet can help reduce inflammation caused by inflammatory foods like meat and dairy. A good reason to restrict animal protein and especially red meats in our diets.

Finally, the big question is, do we trust the results? And how did the answers of the questionnaire, which for Miss Vegan, make it clear she does not eat meats, affect the results? The Viome FAQ page states “We use this information to tailor your recommendations”. It also says that “answering all of the General Questions is required for our Artificial Intelligence to process your results”.

Without access to the raw sequence data, to get a “second opinion”, it is difficult, however, to validate any of the results.