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.