Gut Wars: Diversity

Following on from my recent guest blog for uBiome, I decided to take a closer look specifically at my gut diversity. Here are the counts for comparison between my first test in March 2014, shortly after antibiotic treatment, and a year later in March 2015:

Interesting, I’m sure you’ll agree.

This has me wondering what normal is? I mean, uBiome’s norm when looking across all their samples, I wonder what that looks like. I don’t know the answer to that at the moment, and it may not be that relevant for the average person, but if you’ve been on antibiotics or had some other loss of gut diversity then it would certainly be useful to know. Though even some results from just a handful of “healthy” people would give a fair indication, I’d bet.

It is almost certainly an improvement that I now have twice the level of species diversity I had a year ago (leaving aside which species these actually are, as that is also likely important), but how much further have I to go? Is the norm 100, 150, or 500?

If you’re reading this and you have taken a uBiome test then I’d love it if you posted your stats for comparison. It’s quick and easy.

The easiest and quickest way to find this info is to click “Raw Taxonomy” in your uBiome dashboard. Then Ctrl+F to run a search for “phylum (beware that Subphylum and Superphylum will be counted if you don’t specify the leading inverted commas in your search) and then “class – “order – “family – “genus – one at a time and see how many hits you get in each case. I suggest using Chrome browser rather than Firefox which won’t return more than 100 hits.

Alternatively you can put your results into a spreadsheet, great instructions for which can be found on Richard Sprague’s blog. This option makes it easy to get those counts but also to manipulate your data in any other way you fancy going forward.

So do me a favour and post your diversity counts.

I’ll just finish this post off with a quick look at which of my bacteria went extinct in the last year. Given my diversity has vastly increased, I’m not expecting many. Here’s the species level data (courtesy of Richard Sprague’s analyser):


The disappearance of C. butyricum is interesting, it can be pathogenic but it is also widely used as a pro-biotic in Asia as a treatment for it’s misbehaving cousin C. diff. And as you can guess from its name it is a butyrate producing bacteria. Last year C. butyricum made up more than 1% of my total gut flora, which is much more than usual. Now it is gone. In fact, many of my clostridium have been kicked out, half of these now-extinct species are clostridium, many of which are normal in the human gut but also can be pathogenic. Last year the clostridium genus made up 8.63% of my gut whereas now it is at a normal level (1.56%), so probably good on the whole.

B. catenulatum is gone too, which seems a shame. I guess it has been out competed by the other species of bifidobacterium that I introduced over the last year.

L. lactis, often present in dairy products such as cheese, is gone. Why? No idea.

I’m pissed to see R. bromii is gone. It’s considered a cornerstone species and I was pleased that after my antibiotics, when I first tested, there was a tiny amount still holding on. But now it is gone. Why are my ruminococcus abandoning me? I’ll be looking at which cornerstone species are missing from my gut next. R. bromii is not the only one, and these key species being absent does not bode well for my future gut health.

That aside for now, when you consider that these 19 species pictured above were missing from my second sample, it makes my increase in species level diversity even more impressive! I started with 55 species, lost 19 of these and gained 73 new species. I must be doing something right – or at least, More things right, than wrong!