Should you have your gut bacteria sequenced? Update on uBiome and American Gut

A couple of months ago, I called attention to a concerning matter: a science writer, Tina Saey, reported on Twitter that she received dramatically different results from the two major microbiome sequencing services available, uBiome and American Gut. And what was most concerning was that the two tests were done using the same sample. So any sort of external factors like diet, or simply the passage of time, could not account for the difference. Tina later posted a lengthier rundown and analysis of her experience.

Shortly thereafter, another science writer undertook a similar experiment, but with a twist: like Tina, she sent the same sample to both uBiome and American Gut, but she also sent an extra sample to American Gut that was taken from the same — but a different section of — her stool (sorry, I try my best to avoid the inevitable ick factor). Interestingly, in her case both uBiome and American Gut matched up well. But her two American Gut samples, taken from different parts of her stool, did not. There were a couple of fairly significant discrepancies.

Well, I think it’s time to close the loop on this matter as best we can, as I’ve been getting questions about the usefulness of testing.

A couple of weeks after sounding the alarm here on this blog, uBiome co-founder Zac Apte left a comment here directing people to an informative blog post at uBiome addressing this issue. The main thrust of it is that uBiome believes the discrepancy to likely be due to the fact that they and American Gut use two differing “extraction” techniques, which are known to result in different outcomes. Fortunately, the way these techniques produce different outcomes is well-understood and can be quantified, and so Zac and his team were able to run an analysis to see if Tina’s results matched when corrected using the “extraction bias” information. And they did seem to come quite close:


Furthermore, I queried Zac recently on the case of that second writer and her experiment on intra-stool variation. And his answer was that this is not much of a surprise — intra-stool variation is expected, and that is why these services have specific collection instructions (swabbing toilet paper), so that the same area is sampled every time. So it seems that directly sampling stool, and in two different areas, circumvents the procedure that’s specifically designed to avoid this problem.

So where does this all leave us?

Well, we’re certainly still left with the question of which technique — and thus which service — provides a more useful and “accurate” accounting of your gut microbiota. Ideally, I’d like to see a dialogue between American Gut and uBiome so that we can get a better understanding of all this and get at what’s really going on. A comparison study might also reveal that perhaps something other than the extraction technique is creating the discrepancy, such as differences in transport or collection methods.

But regardless of all that, I think there are two strong reasons to do one of these tests if you are so inclined.

Detecting Extremes

In my opinion, this is the clearest and best reason to plunk down the money for these tests: the chance that you will find something weird and out of the ordinary. Who knows what you might find? That’s really the usefulness of a test that is largely based on comparative data to a broad population. And it seems to me that both services are still capable of surfacing this kind of thing. What do I mean by something weird? Something like an overgrowth of a specific class of bacteria, the presence of something very rare, or bacterial ratios that are significantly outside the distribution of the population to which you belong.

Detection of any of these things are helpful clues that may get you closer to figuring something out. If you suffer from some sort of health issue and suspect a gut bacteria-related connection, and you can afford the cost, then this may very well be a good reason to do this kind of testing.

Detecting Trends

Trending — seeing how your gut bacteria change over time in response to different stimuli and interventions (drugs, diet, etc.) — is the other very good reason to consider testing. Assuming you stick with one company for your testing, you should be able to get a pretty reliable view of how your gut is changing over the course of several tests. Trending might also be useful for trying to connect the improvement or deterioration of a specific health condition to a specific change in your gut bacteria. Also, while we don’t have a ton of clear and widely established bacterial health markers, the research definitely does point to some (and if you’ve been following along, you should know who they are). Which means there are some clear targets for anyone trying to hack their gut.

The one piece of advice I would give in this regard is to always try to make a prediction before testing, instead of trying to make connections in hindsight. It’s very easy to make all sorts of connections and explanations after the fact, but if a prediction made before receiving results turns out to be true, it’s much more likely to be relevant (because it’s so unlikely for it to actually come true).

And on that final note: I’m going to have some pretty interesting stuff to share very shortly. Stay tuned.

— Heisenbug


14 thoughts on “Should you have your gut bacteria sequenced? Update on uBiome and American Gut

  1. I can’t say I’m surprised by a difference, the question is how significant that difference is. But I go along with the view that using the same company each time and the same collection methods ought to avoid major problems.
    I recently got my uBiome results in and they are better than I expected after my almost year long antibiotics kick! Interestingly they tally quite well with what I predicted in certain areas in line with my pre- and pro-biotic use – lots of cool things to see.
    I’m waiting on uBiome to get back to me on why my genus level bacteria in total only adds up to ~70% while other groupings at least get close to 100% (though none actually get all the way).
    I’m hoping it is a dashboard problem where the info from the database is not all displaying rather than the data not all existing in their database!

    • I think I know why your genus level counts don’t add up to 100%. I wrote UBiome with the same question. I presume that your species level counts don’t add up to 100% either – and by a larger margin.

      A fairly large proportion of the gut microbiome species are unknown and there are (fewer) unknown genuses as well. UBiome is looking for a percentage match of the sequence to known species, genus, family,etc. The precision of the match is less the higher up the tree they go. When they lookup your sequence they might not find a hit within the required 97% at the species level – but at the 95% genus level it matches up perfectly. The same happens at higher levels too.

      So, in some situations UBiome knows there is a bacteria there. They don’t know what species it is – but they do know for sure it belongs to a particular genus. In the same way, sometimes they can’t identify a particular bacteria at either the species *or* the genus level – but at the family level they can identify it perfectly. In each of those cases, the bacteria is counted at the taxonomic level where it can be identified.

      I had expected that any missing critters would be identified with some sort of ‘unknown species’/’unknown genus’ place holder at each level, with the associated counts of the unclassifiable bacteria, just to make it clear – but that’s not how they chose to do it. Once you know that count roll up discrepancies are due to unknown taxonomic identifier matches – you can just make that mental adjustment. I even have a missing phylum with a count of five bacteria in mine.

      • Thanks, yes that’s certainly it. I asked ubiome too and got the same answer but forgot all about my comment here. The databases for comparisons are getting better every day so hopefully we’ll see close to 100% species data in a few years.,

  2. You hit the nail on the head – when I tested my kid, we found 2 urease producing bacteria that typically live in the stomach and dilute stomach acid… once we implemented h pylori protocols – the most famous of all the urease producers – we started getting somewhere – we also found 25 species of clostridia – which responds well to chitosan (it breaks down the cell wall) and oxygen therapies along with s boulardi – if you see a urease producer, l. reuteri is effective – so even if you don’t see a lot of campylobacter or ochrobactrum or h pylori – you still should treat it as most of it lives in the stomach lining – also, American Gut will test your mouth and that might be another way to find out what lives in your gut… also, periodically, American Gut restests *the same stool sample* and finds additional bacteria –

    One more hot tip – try using a biofilm buster like serrapeptase prior to using a probiotic/herbal bug bomb – and check out transfer factor isolated from colostrum – if you got crappy gut flora from mom, your immune system might not recognise it as such – so you can use colostrum/transfer factor from a cow/goat and actually retrain the immune system…

    • Too funny! That’s my post and my husband. I never thought I’d see it referenced elsewhere! The reader’s digest version of my husband’s outcome is that as long as he almost exclusively eats lots of organic meat and organic vegetables, and very low sugar and refined starch (no rs specifically, but some white potatoes on a limited basis), he has very few IBS flare ups. Add in beer, sugar and/or low quality restaurant food, and disaster occurs.
      I am here at this website, trying to figure out what it means to have 81% firmicutes in my own gut (and only 10% bacteroidetes). Still not sure if that’s good or bad. Seems to be consistent with eating a diet that includes lots and lots of vegetables in addition to meat (semi-paleo/ancestral diet, in my case).

      • Mariel, what ever happened with your husbands bacteria? I just had a stool sample and enterococcus avium and just wondering if he got his under control.

  3. I was dx’d with Rheumatoid Arthritis in 2008 after a sudden onset flare. Per the work of the late Thomas McPherson Brown (see The Roadback Foundation), I started Doxycycline. I take 200 mg on MWF only. I responded fairly quickly to the protocol and got to remission. That is, very little joint pain, and blood work normalized.

    In the last year or so, my joints have been aching more. One thought is to rotate to a different antibiotic, such as minocycline. Brown did this for some patients, every 6 years or so.

    My MD suggested I add in azithromycin at 250 mg on Tu and Sat, continuing to take the Doxy on MWF. This helped reduce the inflammation in my hands and elbows, but (!), I began to experience very low moods and a marked decrease in appetite.

    About ten weeks in, I dropped the azithromycin. I ordered a test kit from Ubiome.

    I’m not certain I’ve ever been healthy. Formula fed. Standard American Diet. As a teen, back in the 70s, one year had a ruptured appendix, then the next year had serious GI distress & fever while traveling in SE Asia, then the next year hospitalized for an entire month with a staph infection (sepsis arthritis) —IV antibiotics & oral abx for 12 months.

    So in mid-life, I get RA. And I stumble across a protocol that uses antibiotics to get to remission, and it works well for me, until recently.

    I’m just not sure how to proceed. I’m not confident that it’s possible to repair my gut to the point that my RA cools and stays in remission without abx. But, I’m also conscious that the antibiotics cause collateral damage.

    It will be interesting to see what the Ubiome test reveals. I take Bifido Factor by Natren. And Jarrow’s Saccaromyces boulardii. I eat homemade cultured yogurt daily. I make a good effort to eat real food, but with a suppressed appetite, I’m sure I’m coming up short.

    Very interesting blog and comments. Thanks all.

  4. personally I was disappointed with UBiome. It gives such high level classifications. It does not get down to the species level.

  5. Guys – can anyone help with an explanation of the results of my American Gut Sample please? Most abundant were Prevotella and Lachnospiraceae (18.8%), Ruminococcaceae and Order Clostridiales both 13.%. Sentence underneath then says: ‘Your sample contained 9 rare taxa, including the following: (Genus) Clostridium, Actinobaculum, Allobaculum and Alicycliphilus’. I’ve been interested in gut bacteria for the past 30 years, when I developled Myalgic Encephalomyelitis (called (wrongly) Chronic Fatigue Syndrome), following a Coxsackie B virus that showed in my bloods for the best part of a year. Despite vitamins, clean eating, kefir &c I’m no better (and now have to take thyroid medication, and PPi’s for the oesophagitis). Feel like I am getting nowhere fast, and missing some parts of the ‘jigsaw puzzle’ that might see a slight recovery, if nothing else. ANY information would be very much appreciated. Many thanks.

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