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.
I 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.
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.
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).
Species 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).
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.