Why There’s Little Straight-Talk About, Well, Using the Bathroom

A routine activity that’s built on euphemisms

There are people who claim they can tell your fortune through the reading of tea leaves, an art known as tasseography.

As for us, well, we guess you might say we can tell you a lot about yourself by reading your toilet paper.

You see, this is the method of collection we use to collect a gut microbiome sample for our DNA sequencing process. Continue reading “Why There’s Little Straight-Talk About, Well, Using the Bathroom”

Tracking Poop, Gut Parasites, and Antibiotic Effects

At the recent Quantified Self conference in San Francisco, self-experimenter Mark Moschel talked about his unfortunate encounter with a parasite-filled bowl of ceviche in the streets of Ecuador. But in true QS fashion, Mark turned it into an opportunity to learn about his body. He took several uBiome tests, and shares what he learned in the video below. Thanks Mark!

One Week Change In My Microbiome

The inspiring Richard Sprague joins us again, with a curious finding!

Having done multiple uBiome tests over the past year, I already have a sense of what my “normal” gut biome looks like. Although there is a fair bit of variation (especially after my various experiments, like sleep-hacking or jungle exploration), my results generally fit the range of “healthy omnivore”. But most of my tests are taken several weeks or even months apart, where it can be hard to understand precisely what’s driving the overall differences. How much variation would I see between samples taken just a week apart?

To find out, I sent two gut samples to uBiome, one on April 21 and the other exactly one week later on April 28th. I received the results last week, less than a month after submitting them. (uBiome turnaround times are getting much faster!) The overall picture looks like this:



That’s more variation than I expected for such a short time period. What’s driving the changes? Fortunately, the new uBiome web site makes it much easier to compare one sample with another. In my case, it shows the following changes over the week:


These charts show changes in the absolute population of various microbes, which uBiome calculates by dividing the newer sample “count_norm” field by the same field in the earlier sample. Since this tends to give extra weight to the smallest populations of microbes, I prefer to calculate by proportion; in other words, which microbes changed most in overall percentage against my entire microbiome. After downloading the raw data and running it against my open source tools, here’s what I found (at the genus level):

tax_name count_change
Roseburia 41427
Faecalibacterium 33862
Bacteroides 24346
Lachnospira 13601
Lactobacillus 9874

These are all generally considered “good” bacteria, so I’m glad to see the increases. But why the change at all, especially over such a short time period?

Fortunately, I have some additional data.  I regularly track the food I eat using the MyFitnessPal app on my phone. Using a handy data exporter I summarized the macronutrient information like this:

Calories Carbs Fat Protein Cholesterol Sodium Sugars Fiber
Average (month) 1841.7 192.2 102.7 94.9 268.0 2298.5 64.1 15.2
Average (Week) 2242.6 241.9 124.7 108.7 262.3 2814.3 78.3 16.9
Difference from Ave 400.9 49.7 22.0 13.9 -5.7 515.7 14.2 1.6
% Diff from Ave 122% 126% 121% 115% 98% 122% 122% 111%

Looks like I ate more calories than normal that week (that was when the new Chik Fil A opened near us), which explains the higher-than-average numbers for carbs, fat, sugars and the rest.  But there is one unusual result: note that despite my extra appetite (and that Spicy Chicken Deluxe), I ate less dietary cholesterol. Could that explain the increase in those particular microbes?

Of course, this is all extremely speculative, but a quick internet search reveals an intriguing study involving patients with cholesterol gallstones whose microbiomes lost exactly the three microbes that I gained. Is there a link?

Who knows? It was only a week, and it was a pretty small difference. But that’s the fun of experiments like this: “normal” people can make discoveries.  And if I did find evidence of a link between cholesterol and the microbiome, this could have huge implications for the treatment and prevention of heart disease.

Alexandra, you may want to give a heads-up to the Nobel Prize Nominating Committee. 🙂

Meet A Crohn’s Snowflake

josh3This is a guest post by Josh Pate. Thanks Josh!

Crohn’s Disease patients are like snowflakes; we’re all different. There’s no known cause or cure for Crohn’s disease and millions of people suffer silently from it every day with different triggers, different causes of pain, and different levels of sensitivity to food. We’re so unique that it sometimes feels like no one understands our individual experience with the illness.

Living with Crohn’s Disease can be really painful and embarrassing, but for me the worse part of it all is not knowing how to make it any better and feeling alone in the fight.

Crohn’s is an inflammatory bowel disease that affects patient’s intestines, stomach, and more. Millions of people all over the world have Crohn’s and about 75% of patients that have one surgery will end up having at least one more in their lifetime. I’m 24 and I’ve already had 2.

Every Crohn’s patient is different. Some can’t tolerate chocolate, while others find spicy foods set them off. Fried and greasy foods are particular triggers of mine while stress, lack of sleep, and poor diet are thought to be common triggers for scores of Crohn’s patients.

While any Crohn’s patient out there will tell you that careful attention to diet can lessen the symptoms or even send a patient into remission, every doctor I’ve had ignores that subject and leaves that discussion up to a nutritionist. Environmental factors often get put on the back burners when doctors start prescribing steroids and immunosuppressants in order to put the disease in check, but often being aware of your condition and journaling lead to mini personal breakthroughs where patients find what works for best for them.

Hippocrates once said, “Let food be thy medicine and medicine be thy food”, which is such a sublime statement. While food alone is no substitute for medical treatment, the truth is that we are starving for more data – more medicine, more knowledge – that we can use as patients to make informed decisions about our care, our diets, and our lives.


I am hungry for more ways to quantify how my disease affects my life, and vice versa.

That’s why I am using uBiome tests to track how I’m feeling during flares. I feel like using this data point of the microbiome in concert with the piles of other data that I’ve been collecting like food journals, complete blood counts, as well as activity and wellness journals, will lead to personal health discoveries. Little Eureka! moments.

Josh’s intention is to collect as much data as possible in order to empower himself to make informed decisions along with his doctors, so that in the future he can take control of life and disease. If you’d like to follow Josh’s experiences, check out the uBiome newsletter for updates or subscribe to his TinyLetter here – https://tinyletter.com/crohns.

Free uBiome Gut Kit For Inflammatory Bowel Disease

picnichealthWe’re excited to announce that uBiome is partnering with PicnicHealth, a service that gathers and manages all your medical records in one secure place.

If you have inflammatory bowel disease (IBD), we invite you to:

  • Join the uBiome IBD study to help understand the role of the gut microbiome in this disease
  • Have PicnicHealth gather medical records from your GI doctors and create a single, aggregated medical record that you can securely access
  • Get a FREE uBiome kit to discover your gut bacteria (first 250 participants only, use code PICNICBIOME5 at checkout for your free kit)


Results from the study will be used to advance IBD research. Please join us today, at no cost to you.

Learn more at http://ubiome.com/pages/picnichealth.


Gut Wars: One Man’s Adventure With Antibiotics and Ulcerative Colitis

This is a guest post by Clark Ellis, who has studied his gut through antibiotics, ulcerative colitis, and recovery. 

(Disclaimer: uBiome is not a diagnostic test. This is an example of one’s person’s story of self-experimentation and personal research. Please see your doctor if you have any health concerns. uBiome does not endorse any course of treatment nor offer medical advice.)

Thanks so much for sharing your incredible story with us, Clark!

Last year, following a lengthy course of antibiotics, I had my first uBiome test to survey the damage to my gut. Unfortunately, the antibiotics resulted in me developing ulcerative colitis, an inflammatory bowel disease. I managed to get into remission by improving my diet and taking a decent Bifidobacterium supplement. While well on my way to remission I took that first test. The results gave me hope as many of my friendly gut bacteria had survived their ordeal — though they had been decimated — you can read about those test results here.

Last year I enjoyed a summer without colitis, and then stopped taking the Bifidobacterium supplement and began taking a different probiotic containing Lactobacilus and Streptococcus. This is when things went horribly wrong for me.

Within a couple of weeks I had a flare of ulcerative colitis. Could it really have been triggered by the Lactobacillus and Streptococcus supplement? Or had the Bifidobacterium left my body when I stopped taking it, resulting in a flare? Or was something else going on?

I recently took my second uBiome test to help me figure this out and see how far my gut has recovered from the damage caused by the antibiotics. Here are the results.


The latest results (along with last year’s result in parentheses).

Firmicutes: 62.9 (66.1)
Bacteroidetes: 30.9 (28.7)
Verrucomicrobia: 2.49 (1.86)
Actinobacteria: 2.25 (1.29)
Proteobacteria: 0.483 (0.0889)

These are my top five phylum level bacteria. When you compare these results to the average, it’s clear that Proteobacteria is too low; one seventh of uBiome’s average norm; but it has increased significantly since last year, so may not be a long-term concern – it is heading in the right direction at reasonable speed.

The portion of Firmicutes and Bacteroidetes are roughly the same as before. The major difference at the phylum level is that I have more Actinobacteria than before. I also have more Verrucomicrobia than last year.

So at this high level, I’m pretty pleased with the improvement.


But the devil is in the details, so let’s take a look at what’s going on at the deeper genus level. In my original post following my first uBiome test I singled out five key genera of bacteria that I saw problems with. Let’s see if I made any progress:



This genus is like Rocky Balboa; you think he’s out for the count, and then he pulls off a miraculous comeback. Last year Pseudobutyrivibrio was out for the count and I thought it likely that it would never recover; a year later, it’s normalized. It was just 0.0764%, at the very bottom end of the normal range and way off average. You can probably guess from its name that it is a butyrate-producing bacteria and since butyrate is considered to be important in protecting the colon I was keen to nurse this genera back to normal levels. I now have a whopping 2.81% of this stuff in my gut, which is above average. A great start then.



The Bacteroides genus makes up 28.1% of my total gut flora. That’s still way higher than normal, and essentially static from last year (28.3%). I hope in time to see that drop closer to the normal range, the top end of which is 18.2%. But I don’t think it’s Bacteroides that are the real problem here; it is not that they are too high, but rather that other genera which normally make up 10-25% of total gut flora are absent or much too low, as I’ll show you further down.



The supplementation has clearly worked. According to my first test, the only bifidobacterium present was Bifidobacterium catenulatum. But my gut needed all the help it could get and I wanted to see if I got benefit from increasing this genera and diversifying the Bifidobacterium species. I believe it did help me get into remission from my ulcerative colitis, and it is helping me once again get out of my current flare. Slowly. I think it is significant that I went into my second flare about a month after I stopped supplementing with it. As a result I did not take any probiotics for two or three months before this second test – so whatever appears in this latest test is a true resident, not a passer-by. The result? 2.17% (almost double what I had a year ago).

Looking briefly at the deeper species level in the raw data file, whereas last year I had just one species flying the Bifido flag; I now have a dozen! All those in my probiotic are represented as well as a couple of others that have appeared from somewhere.

I have slowly improved in the two months since this test sample was taken, and have almost no pain now. I put this improvement down to me having started the Bifidobacterium supplement again.

But the probiotic supplements available on the market only represent a tiny portion of our usual friendly gut residents. What are available is no panacea, and what works for one person might not work for another. However, of greater concern, is that it seems to me supplementing can sometimes make things worse!

I was taking a Lactobacillus and Streptococcus supplement in the weeks leading up to my current colitis flare, and it seems it may have triggered it.

Yesterday, to test that theory, I took a single capsule of that probiotic mix again. The result? Six hours later I began getting pain in my colon again for the first time in a month, in exactly the place where I have had ulceration. The reaction was so quick and strong that it is clear to me that this Lactobacillus and Streptococcus probiotic does not agree with me. While the Bifidobacterium probiotic has been welcomed by my gut as a permanent resident, my gut does not seem so welcoming of the Lactobaccilus and Streptococcus supplement.

I also took some friendly E.coli supplements last summer, which have been shown to help some people with ulcerative colitis, but they haven’t shown up in my test results. I’m a little surprised at their absence. There are a number of unclassified bacteria in the sample – around a sixth of total at the genus level; do these other probiotics lurk in there, currently unidentified? Or perhaps they simply didn’t hang around and become resident.



Remember Roseburia from my original test? Last year it was dangling by its flagella; but now it’s alive and kicking and at normal levels. With the R. hominis species being studied as a potential treatment for ulcerative colitis, I am really pleased with how well it has rebounded from those antibiotics.



Alright, it’s not all good news. I am obviously disappointed with this result. I had hoped it would rebound as Roseburia has but unfortunately it is still struggling. It’s supposed to like resistant starch, but that hasn’t worked out for me as I do get a lot in my diet. As you can tell from the name, it is a bacterium commonly present in grazing livestock. I won’t be eating grass, but I will be eating greens: kales, beans, broccoli, maybe even some salad (not a big salad eater). I’m also going to be trying out brown rice, as I get on well with white rice already and Ruminococcus is supposed to like whole grains. So Ruminococcus is very much still on my ‘to fix’ list, and I hope next time I test it shows a good improvement.



This genera is still present in large quantity but has normalized, dropping from 20% down to 14.3%. All good.

So what have I learnt about gut flora following antibiotics?

Some genera — such as Pseudobutyrivibrio and Roseburia — have a remarkable ability to rebound back to normal when they look like they’re all but dead. Others are able to normalize, even if you would think the opposite would occur based on your diet; such as Faecalibacterium. In terms of other major players however — such as Ruminococcus — things are not so easy to fix.



As well as Ruminococcus, I’m adding Dorea to my concerns list. It’s barely alive, but potentially important. It was completely absent from my previous test. In common with Ruminococcus they both have normal ranges (demonstrated by the green area on uBiome’s charts) that begin above zero, so my result being almost zero is definitely a problem in my interpretation. Many other genera have normal ranges starting near zero as you will see below in a moment, so are less worrying to me.

Overall, you can see the improvement on the bacteria I have been focusing on, and for a year’s work on my gut, I’m pretty happy with the results.

But there are still problems. My gut is like an old roof: I have fixed (or am in the process of fixing) some of the main beams, but there are still a few sizable holes, and just as importantly there are many, many tiny holes collectively letting a lot of water into the house. I see this problem as being the ultimate cause of my ulcerative colitis. These genera of bacteria that are usually present in small numbers may collectively be very important. Not only can we not get them in supplement form, but we also know little about them. People (including me) tend to talk a lot about the genera and species that have been researched, but there are loads we know little about and there is plenty of scope for them to be important. Vital even.

Below are the last few entries in my report, at genus level. You can see that many of them are at the bottom end of the normal range, and way off average. This is what around 30 of my results look like (out of 65 genera in the sample) and they are all the same – on the order of twenty times lower than the average. That cannot be good for my gut.


But the geek part of me was pleased to see this. My first test with uBiome proved that their tests are accurate – I expected damage from the antibiotics and that’s what the results showed. This second test proved that uBiome’s tests are consistent; I expected some improvements but for continued signs of damage, and that’s what these results show. That makes me really happy as we aren’t wasting time and money. Well done uBiome!

Contemplating my gut metaphorically, I hope that having fixed some of the roof beams and patched up a few of the bigger holes, that with some good weather, the rest will sort of, well, fix itself… I doubt that works for roofs, but maybe it will work for guts.

We’ll find out later this year.

The Case of the Curious Microbiome


Meet Siavosh. He’s the data scientist behind last week’s popular post on male vs. female microbiomes.

Siavosh grew up overseas, got his PhD in Physics from Stanford, and is now an amazing part of the uBiome team. His desk is right next to an impressively high window that streams in sunlight and looks out over the city of San Francisco.

During a conversation near this window, we decided to start digging into the microbiomes of the fine folks who work here at uBiome, to see what we find and share it with you. Siavosh bravely offered to go first.

Here’s what we discovered in looking at his gut microbiome data:

Screen Shot 2015-02-23 at 6.32.33 PM


The charts above show that Siavosh’s level of Bacteriodetes is elevated far above what we would expect in the anonymized, aggregate uBiome dataset.

What about the error bars, you might be wondering? Well, the figure below shows that the prevalence of Bacteriodetes is 22% +- 13% in our dataset. In other words, the 68% confidence interval for the mean of Bacteriodetes is 9% to 35 %, and Siavosh has 38%.

Screen Shot 2015-02-23 at 4.32.37 PM

Why is he so different?

Differing levels of bacteria in the gut are known to be affected by a number of factors, including diet, exercise, health conditions like Crohn’s disease and depression, and even where we live and grew up.

One possible explanation for his outlying data is that Firmicutes tend to be more prevalent in obese people, and Bacteriodetes more prevalent in lean people. (He’s on the leaner side.) Growing up in Iran could also have had an effect, as well as the differences between his diet and the traditional Western diet.

We’d like to open this up to our readers too. Can you think of other possible explanations for Siavosh’s gut being enriched with Bacteriodetes? And better yet, would you like to add your microbiome to the mix, and see what mysteries lie in your gut? Find out what’s different about you!