The Gut Following Antibiotics: My uBiome Results

That cannot be right!

That was my first reaction when I saw my uBiome results. Having just come off almost a year of potent antibiotics, I had prepared my eyes to view a ragged, threadbare landscape, but what I saw – glaring problems aside – was diversity!

Further detailed viewing has convinced me that the results are accurate.  They need to be nurtured as some genera of bacteria are only hanging on by their pilitips [erm, is that a new word? I’ll be covering neologism – the creation of new words – in my next post] but the bacteria are still there. It’s possible for me to reclaim my gut!


I have myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), a disease which is strongly linked with poor gut health. I could go on and on about that, but instead I will just point out that the world renowned virus-hunter, Professor Ian Lipkin (think West Nile virus, SARS and Ebola) believes the cause will be found in the gut, and a crowd-funding campaign is under way to raise the $1.3 million needed to enable his team to do the work. Please do check out The Microbiome Discover Project for further details, and if you want a detailed understanding of the study then Simon McGrath does an excellent job in his article on Phoenix Rising.

antibiotic-bombI also have a suspected bacterial infection: Bartonella and Borrelia (Lyme disease) and as a result I endured almost a year of antibiotic treatment (Rifampin, Clarithromycin and Ketek) before which I had a gut flora test with Red Labs in Belgium.

While on the antibiotics I developed ulcerative colitis (UC) and lost 45lb over a few months. Standard treatment failed to make any difference (Mesalazine and Prednisolone) and eventually I decided to stop the antibiotics out of desperation. My weight lost halted immediately and I am slowly making a recovery.

It seems the antibiotics were a significant trigger of the UC and certainly perpetuated it. I took a uBiome test to see what damage the antibiotics did and now I’m trying to rebuild my gut.

Diet before the test

I have to admit that initially the improvement in my diet was not really by choice. When the UC hit, it came with significant intolerance to a variety of foods. I can no longer eat wheat/gluten, eggs, dairy (except cheese), maize, and almost all additives are out too. If I eat any of these then I have a strong and immediate flare. I eat oats and rice, meat and root vegetables. Some fruits are okay, some are not. A cup of tea of coffee will likewise leave me a wreck for a week, so I just drink water.

So I eat a lot more fibre than I used to and I no longer eat any junk at all. The only treat I have is dark chocolate, with no soya lecithin included, and this of course is an excellent pre-biotic. So I’m neither a healthy omnivore nor a Paleo-dieter, but perhaps somewhere in between the two.

Throughout the time I was taking antibiotics I was taking a pro-biotic supplement (Vitafytea bififlor forte).

Preparation for the test

I had been off the antibiotics for about a month when I took the Ubiome test. I knew I wanted to increase my dedication to my gut, introducing more fermented foods, pre- and pro-biotics, but I didn’t want to screw the results up and just see what was transient in my gut. So I held off introducing more until after the test. The results of this test will show me what the antibiotics left me with and only the very beginnings of my rebuilding.

I stopped the bifido pro-biotic supplement two days before my test. I had a pretty fast transit time at that point, so the results should be a pretty good reflection of what is at home in my gut, post anti-biotic treatment.

The results

As I mentioned already, before starting antibiotics I had a gut flora test with another company. This does allow me to make some comparisons, though being a test with a different company, with different processes, you have to take the comparisons with a pinch of salt.

Bacteria are grouped together at different levels (phylum, class, order, family and genus).  My top 5 phylum-level gut bacteria are shown in the chart below, and the grey-scale image shows the same from my earlier Redlabs test. Note that the ‘Average’ column is based on uBiome’s entire database, including both healthy and unhealthy folk, so may be somewhat misleading.


The average given is from uBiome’s ‘healthy omnivore’ data.

Bacteroidetes are normally considered to be quite resistant to antibiotics, but mine have more than doubled. And firmicutes, which are normally thought to increase under antibiotics, and thrive when fed fibre, have instead decreased. You can see why my initial reaction was to think something was wrong with the results.

But the real interest, for me at least, is at the deeper levels. At the genus level for instance, I found that I have a dozen bacteria that are way below the normal average, either right at the bottom end of the range of ‘normal’ results, or below.

uBiome are still developing their visualization tools, as well as the size of their database, so in the future it’ll be possible to see how results compare to others that have taken antibiotics, but unfortunately this is not possible just yet. For now, I’m comparing my results to ‘Healthy Omnivores’ and ‘Paleo Dieters’ as seems most appropriate.

Here is a typical example:


This suggests to me that the antibiotics did some damage and the additional consequence is that the genera of bacteria that are more prominent, as a percentage look very large, but not necessarily because their numbers are truly that high but because there’s a lot else missing, skewing the results.

When I test again, later in the year, I’ll be interested to see if these under represented bacteria stage a recovery and that’ll be the focus when I look at this next time. This time though, I’m going to point out a few other things that stick out.


Research on Bacteroides is mixed; whatever your view, it’s pretty easy to find a study or two to support it. Some species subclasses are known to be enterotoxigenic and are associated with colitis (Rabizadeh S et al). Given the normal healthy average reported by uBiome is one third my reading, this does leave me wondering if this might be a significant factor in my developing colitis, especially when you bear in mind that my pre-antibiotic test with Redlabs showed a much lower reading of 12.58%. I’d be interested to hear what readers think of that.


Not bad. My Redlabs test reported zero. The Redlabs test appears to be set-up to look for overgrowth rather than undergrowth, so I think the zero reading really meant close to zero. In any case, I have a healthy level now which is likely a combination of supplementation and diet improvement. I hope to increase this further as most research concludes that Biffidobacteria are a keystone of gut health, with other genera of bacteria feeding off the by-products of this bacteria (De Vuyst L et al).

RoseburiaSpecies of Roseburia are known to produce butyrate, which is thought to protect against colitis, so you’ll understand this is one I hope will thrive in my new gut. It certainly ought to represent more of my gut than it currently does.


Ruminococcus should thrive under a diet of resistant starch (Ze X et al). I hope so – as you can see it is rather lacking at the moment, and as I can’t tolerate lentils, beans or most grains, it looks like it’s going to be down to the resistant starch.


I appear to have a more Faecalibacterium than normal, and this may be in part due to their love of resistant starch. One species of this genus, F. prausnitzii, is very abundant in all humans and its relative absence has been linked to Inflammatory Bowel Diseases (IBD). In unison with E.coli, it may even allow IBDs to be distinguished from each other and from those without such disease (Lopez-Siles M et al). 

What next?

My greatest fear was that some types of bacteria would be entirely absent, destroyed by the A-bombs I had dropped on them, but instead I find myself reassured; damage, yes, certainly; but gone all together? No. I have something to work with.

Since I took the test I have taken things a step further. I started growing my own vegetables. I wanted to increase my exposure to friendly soil-based organisms. Working an organic vegetable patch should help my gut, especially if I eat some raw, and ferment my own produce. I bought a fermenting crock and have already started eating home-made sauerkraut. I might write about the science of that if there is enough interest.

As well as this improvement in diet, I started taking various pro-biotics. Mutaflor (a friendly E.coli strain) has been shown to maintain remission in UC, and I bought the strongest bifidobacterium powder I could find from Custom Probiotics. And in light of my results, where an appropriate pro-biotic is available, I intend to start ingesting some, and the CFSRemission blog has some good information on probiotics – the problem is that the probiotic market only represents a narrow range of the different types that should live in your gut.

My diet is already pretty high in resistant starch as I eat a lot of green bananas, cooked-and-cooled potatoes and rice. But having read a lot of good about resistant starch on Phoenix Rising and on Mr Heisenbug, I introduced it as a supplement as well. I also added a FOS supplement and tried apple pectin powder too, but found this hard to swallow. My next test, which I will probably take in a couple of month’s time, will give a much better picture of my attempt to rebuild as it’ll reflect these additions.

So do I think a uBiome test was worth it? It’ll be really good once they’ve developed their tools and algorithms a bit further, but yeah, I reckon it was a very good purchase. You can buy yourself a kit from their website, but before you do, please consider making a donation to the Microbe Discovery Project – the millions of people with ME/CFS have waited a long time for a top scientist to take an interest, but without any government funding, they need your help.

You can follow my blog if you want to see my next results when they come in (buttons at the top of the page). If you’ve got any tips, observations, or questions, please leave a comment below.


19 thoughts on “The Gut Following Antibiotics: My uBiome Results

  1. Thanks for the blog on your abx experience. Funny how you don’t run into articles like this until after you’ve tried it yourself. Me only 2 weeks xifaxan. Now every post I read is “DON’T DO IT” My adverse symptoms are probably in my head. I all the sudden feel more depressed than I used to. Specifically this awful anxiety which passes if I just ignore it. Sorry about the UC. How did they diagnose that anyways? I’m mixed about the lipkin Study after the fiasco at the Peterson institute and I read that they owned a for profit company that did testing on xmri. I read his credentials and they seem impeccable just I’m a little jaded after almost 18 years now. And seeing all kinds of vultures circling over our dying carcasses. I might end up donating some money after I find out a little more about it. I hope he doesn’t give up. He’s trying to get blood out of a turnip though most of us don’t have any money and nobody else gives a rat’s ass. Funny all the billions in federally funded studies and those stingy blankety blank fat cat hard nosed Pri_ks at the cdc & ins can’t fund a major study on a shoestring budget that might yield ground shaking paradigm change in the way we think about ME/CFS. (and possibly a lot of other conditions) Almost seems like there afraid he might succeed.


    • I do know others who had similar situations to me who improved on abx. Don’t think getting UC from it is all that common but it can happen. Hindsight is a wonderful thing. We can only educate ourselves and make the most informed choice we can.

      Usually they diagnose it with a colonoscopy, where they sedate you (though that never works for me!) and insert a camera. Because I wasn’t sedated as I was supposed to be, I remember it all. It looked dreadful in there. Terribly swollen and ulcerated. They take biopsy samples along the colon and a little way inside the small bowel as well.

      Sorry you’ve had to wait so long for someone top-class to look at ME. Lipkin is it. There’s nobody better out there. If we enable him to do the research he will find cause of our illness, and as you point out it could be ground-breaking for a lot of other illnesses too.
      It should be the govt paying, they have a lot to answer for, but we can’t change that. It shouldn’t be, but it’s down to us patients. We tell people and many won’t care, don’t realise it could be them, their child dying of ME, but some will care, and will donate what they can and it’ll get done.


  2. Given the clear cause of your UC have you considered a microbiota transplant?

    People with UC has good results with it(and according to some studies it works also for ME/CFS)


    • Good question Viktor. The answer is that I’ve thought about – looked into it quite a bit actually – and decided not to, not yet anyway. I plan to write about that sometime too, where I’ll explain in detail why not. fecal transplants interest me a great deal though.


  3. Did your UC clear up? It takes me about 4-6 weeks to go into remission from antibiotic induced UC.
    I have had 3 flairs and it goes away with probiotics, antifungals and time. In many ways the UC was worse than the CFS.


    • Yes and I found Bifidobacterium probiotics help. But I had a flare start up at Christmas – on my way out of that at the moment. See my recent posts for details.
      So you are the first person in contact with who also has CFS and UC – and like me, induced by antibiotics. I haven’t explored the fungal side of things but know I need to. What can you tell me about it and which antigen gals are you using?


  4. Hey – I did Ubiome 6 months ago, and my

    Bifidobacterium was 7.91% whereas the average sample was 1.14%, and yours was 1.10%.

    Lactobacillus was 0.00% whereas the average sample was 1.06%, and yours was well, not listed.

    It makes some sense as I don’t eat/can’t eat without pain any traditional probiotic food such as kefir, yogurt, sauerkraut.

    I know you aren’t a doctor but most doctors don’t know or understand gut biomes. I still have more tests to do with my doc. But any thoughts?

    It seemed to be the most surprising result from uBiome. I’m not sure what to do to fix it, given a host of stomach pain/extremely limited diet that I operate with, like you no coffee, no tea, no processed sugar, no fruits….etc. Tried OTC probiotics, no effect, felt slightly worse with them. Couldn’t tolerate more than once a day.


    • It’s complicated, I don’t know if anyone fully understands it yet (myself included). I recently did another test and my bifidobacterium was up to 5.22%. Last year it was close to nil. So what changed? Did I eat loads more fermented foods or take supplements? Nope. I’ve taken no supplements and I haven’t changed my diet except to cut yogurt OUT of my diet entirely. Seems to make no sense.

      I do have a small amount of lactobacilus now. Think similarly small number to my test last year, and earlier tests were smaller still or non-existent.

      My diversity has increased though, that’s been a consistent finding over the last few years, I lost loads of diversity when I got ulcerative coltiis, and since then diversity has gradually improved.

      And this is matched by the fact I can eat a lot more now. coffee, tea, sugar, fruit, bread, other gluten containing products…I still cannot tolerate preservatives, they very quickly make me unwell. I think preservatives are very bad.

      What worked best for me to improve (not fix) my gut was to do a very strict elimination diet, totally avoid all the stuff that you can’t tolerate. After a year try a little of what is on the exclusion list to see if things have changed or not, if they have then try slowly reintroducing that item, one at a time, if you get a reaction cut it out again for another year. It sucks a lot when you can’t eat much, I was able to slowly improve that, thankfully.

      And pretty much don’t bother with probiotics. They don’t seem to stick (which may in fact suggest you body doesn’t even want them around!), they often cause people more problems than they fix, and they are just such a tiny part of the overall gut flora anyway that it’s really nowhere near as important as people think. Probiotics available on the market are a bit like adding a little mustard to a cheese sauce – sure, it should probably be in there, ideally, but it not essential and more importantly if the bigger ingredients are absent the sauce is going to be terrible. No cheese? No milk? What are we even making now? Doctors don’t seem to recognize what a minor player lactic acid bacteria are in the grand scheme of things. The focus is simply because they are easy for us to grow and we use them in food production so much, if not for that there wouldn’t be much focus on them when it comes to gut health in my opinion.

      I wish you the best of luck, I have a lot of sympathy for you suffering from gut problems.

      Liked by 2 people

      • This is very helpful iamclarkellis for taking the time to reply. Do you view powerful probiotics like VSL3 the same way?

        I’m doing a SIBO test shortly. Depending on what it says and what my GI says, if we go the antibiotic route, my instinct based on what I’ve read is to rebuild bacteria with VSL3, along with the stuff I am already doing (eating vegetables, no processed food, etc…).

        I’d been taking OTC probiotics from Amazon for the last 3 months, but didn’t feel any better. If anything, I felt slightly worse. I was taking them first thing in the morning, just before breakfast (usually just a plain, natural, soft granola bar). I stopped taking probiotics about 2 days ago, because of the reasons you listed, and because I was showing no improvement.

        No GI I’ve talked to seems to be able to answer a seemingly basic question – if we use antibiotics, or conditions like UC reduce our bacteria diversity – and we switch our diets but aren’t improved – how can we reintroduce the good bacteria, short of an FMT, if probiotics only have a couple strains?

        Liked by 1 person

      • While VSL3 does contain higher numbers of bacteria than some other brands, and are more diversity than some other brands, none of the brands on the market, including VSL3 offer anything but a very narrow band of bacteria that is nowhere near representative of natural gut flora.

        That doesn’t mean to say they aren’t worth taking, people may get some benefit out of them. Have a go. And maybe they will stick in you better than in me. I’d be interested to find out. But when you take probiotics all you are taking are the species that are in them, when chances are you also need lots of other species that are simply not available anywhere on the market. It’s like cutting down every tree on earth, all the many different types, then you repopulate by planting with the seeds you have but all you have are Oaks Birch seeds. An improvement, maybe, but where is the Ash, the Beech, the Chestnut, the Maple, Willow, and all the other thousands of trees? You just can’t get hold of the seeds. The GIs don’t know, most of them anyway, because its not their area of focus. All they tend to know about pro-biotics is what the public read in the press, which is junk information really.

        Good luck sorting it out, or at least finding something that gets you headed in the right direction. I look forward to poo-pills with all the different bacteria present that we need, but for now there is only so much you can do in terms of repopulating your gut flora.

        Liked by 1 person

  5. Pingback: Gut Wars: One Man’s Adventure With Antibiotics and Ulcerative Colitis – uBiome Blog

  6. You should customize probiotics along with a subscription plan.
    Make all the strains match the healthiest, happiest, oldest people’s gut flora. It’s genius. I’ll take my cut in cash please.


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