uBiome making good on their word: more of my gut flora have been ID’d

Eggerthella: one of the newly identified residents of my gut

Eggerthella: one of the newly identified residents of my gut

True to their word, uBiome have been making good on their promise to further improve their algorithms which identify and assign your gut bacteria to their taxonomic ranks. Several weeks ago I wrote about the missing portion of data in my uBiome results, which was particularly stark at the genus level. Back then, only 73.68% of my genus level bacteria were classified. uBiome told me they were continually adding to their database of microbes and improving the algorithms that identify them. Now, 80.284% has been assigned. So we’re getting there at an okay rate. We’ve gone from a quarter missing down to a fifth. Good job uBiome.

In most cases this is due to completely new genera of bacteria being identified; here are all the new ones that presumably will show up on everyone’s reports, provided any are present in your gut (family name in parentheses):

  • Eggerthella (Coriobacteriaceae)
  • Flavonifactor (unclassified Clostridiales)
  • Erysipelatoclostridium (Erysipelotrichaeceae)
  • Turibacter (Erysipelotrichaeceae)
  • Dielma (Erysipelotrichaeceae)
  • Dialister (Veillonellaceae)
  • Veillonella (Veillonellaceae)
  • Megasphaera (Veillonellaceae)
  • Bilophila (Desulfovibrionaceae)
  • Actinobacillus (Pasteurellaceae)

There are a couple of other very minor changes that are a refinement of decimal places, with some going from 0.01 down to 0.00400 and some others going up, e.g. from 27.9 to 28.0. I expect there may be some additional movements like these going forward.

So where does this leave me?
All of the new ones above are normal, or high in number. Erysipelatoclostridium for instance, is more than 9 times the highest end of normal (healthy omnivores). Although I may need to address these, I’m not going to focus on them in this post. My first effort to fix my gut is to nurture the things that are low, then I’ll deal with anything left which remains too high. I’ll probably write about which of my gut passengers might be pathogens at a later date, but for now I’m focused on what’s low.

I previously did some analysis of my gut results following antibiotics, and have now taken a closer look, including all this new data. Things are still subject to change because that missing 20% should appear at some point and genera that are currently low might suddenly climb as a result. But taking the data as it is at the moment, these are the things that I am very low in, and which the antibiotics obviously beat the crap out of:

The Low List
– Roseburia (0.147%)
– Coprococcus (0.113%)
– Pseudobutyrivibrio (0.0764%)
– Streptococcus (0.0664%)
– Ruminococcus (0.0161%)
– Anaeroplasma (0.0121%)
– Butyrivibrio (0.0121%)
– Rhodanobacter (0.00400%)
– Phascolarctobacterium (0.00400%)

– Anaerococcus (0.00400%)
– Subdoligranulum (0.00400%)

Eubacterium is also low (0.179%) but nowhere near as bad as those listed above. My guess is that Eubacterium will recover without much tailored effort on my part. Some of the others are going to be much harder to restore to normal levels and may need specific intervention.

My biggest concerns are Roseburia, Ruminococcus, Rhodanobacter, and Coprococcus; these are not only very low compared to the average norm but are also well outside the normal ranges too.





For the others that are low, the normal range (in green) includes values as low as zero, suggesting that my very low values could be considered normal, even if well below average. Here is such an example:


I’d imagine that many or most of these are in fact not normal but represent the reality that many of us are routinely on antibiotics on a regular basis and have poor diet; I’ll be much happier if these move closer to the normal average.

I am sure biffidobacterium would have been present on the low list were it not for my taking a biffidobacterium containing pro-biotic all the while I was on antibiotics. The same pro-biotic tablet (Vitafytea bififlor forte) only contained one biffido species so I still feel I need to diversify there and am now taking a potent five strain powder. The pro-biotic tablet I had been taking also contained Lactobacillus rhamnosus and Lactobacillus acidophilus. L.Acidophilus is something I want to avoid now because of its negative impact on E.coli, many strains of which are good to have. But I should have some Lactobacillus in my results but they are not showing up – my bet is that they are in that missing 20% at the moment *sigh*. Can’t uBiome order some common pro-biotics, sequence them and then add them to their database? Wouldn’t that be easy? Well until Lactobaccillus shows up, I can only guess and I may well start taking a multi-strain Lactobacillus powder.

Bifidobacterium and Lactobacillus aside, most of the bacteria I am low in are not available in a pro-biotic supplement. Many have not even been well researched, meaning it is difficult to decide what pre-biotics and diet modifications you can make to nurture them. Animalpharm has a load of good information, including this page on Roseburia, so that’s something I’m digesting at the moment, but I’ll need ideas for the others too.

So this is a plea to readers: if you know anything about how to nurture these small numbers of survivors on my ‘Low List’ then please send me a message, tweet me, or leave a comment at the bottom. Thanks.

uBiome are also improving their visualization tools. They’re still not fully-baked yet, but I like the way they’re going with it. Lots of power to compare between your own results, including different types of tests (nose, skin, mouth, gut, genitals) and with other groups of people (different diets, drinkers, weight changes, antibiotics), and they appear to be giving some kind of indicator of sample sizes in these comparison groups too, which is important.

New links to relevant external content have appeared as well as a ‘community content’ heading – nothing in this last one yet, but I look forward to what might appear here in the future.

The one thing missing is disease groups. I know that uBiome will have already ruled this out as they don’t want to fall out with the FDA as 23andme have. But perhaps they could allow users to create their own tags to their samples and for those tags to be optionally public and searchable when others are adding tags to their own samples. This would allow people to make comparisons independent of uBiome specific labelling, and would also allow more unusual sample types to be compared more easily; for instance, the lovely Dr Grace suggested via Twitter that I might want to test the soil in my garden where my home-grown organic veg grows. I think that’s a fantastic idea because my main motivation for growing the veg in the first place is to expose myself to friendly soil organisms that I might lack. It would be handy to know for sure what exactly is in there and up for grabs!

If you’re interested in finding out what’s in your own gut, so you can start charging rent or hand the nasties an eviction notice then you can get a kit from uBiome’s website; but before you do, please check out and consider making a donation to the Microbe Discovery Project – the millions of people with ME/CFS have waited a long long time for a top scientist to take an interest and now they have the ‘Virus Hunter’ Ian Lipkin, but without any government funding, they need your help to fund this world class study of the gut.

Thanks, I appreciate it.

DjangoOh, and those share and follow buttons you’re looking for…those are below if you’re on a smartphone or at the top of the page if you’re on a computer…over on the right hand side…no, your other right. That’s it, you got it.

Image credit: Complete genome sequence of Eggerthella lenta type strain, Standards in Genomic Sciences


One thought on “uBiome making good on their word: more of my gut flora have been ID’d

  1. Hi, love your blog, i geek out on this all the time too. I consume 4tsp of Maya superfood powder every day, my blautia and roseburia are super high, as are my bifidobacteria (i dont supplement my diet with anything except maya powder) get in touch with me and ill send you a sample so you can see if it makes a differnce in your gut!


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