Ubiome Post Intervention Data

Ubiome post intervention

Recently I set out on a mission to fix my gut.  I hoped to improve my food intolerances and clear up my skin. Compiling quantitative data was important to me during this process.  Going into this process I knew my data wouldn’t be proof of any one thing because I changed so many variables at once. Nevertheless, I wanted to see how my changes and interventions affected my actual numbers.  With the advent of a cool start up called Ubiome I was able to sequence my gut micro-biome pre and post intervention.  In addition, I would be making qualitative observations and reporting on those.  In this post I am going to present my data and share my experience.  To get caught up on this entire process, read the two previous posts on this topic.  Here are the links to those:

Poop: How to Create a Good Poop

My micro-biome Data is in; I Need a Recount

Get tested!: For a 10% Ubiome discount use my referral link

I knew something was off as soon as I received my initial data from Ubiome.  My data showed a huge variance from normal populations. The photo on the left below compares my sample with all of the other samples collected by Ubiome, which I believe is approaching 20,000.  It’s a decent sample size to compare to.


Screen Shot 2015-04-14 at 7.04.15 PMPre intervention data as Percent



Notice the Red and Green slices of the pie chart.  In general, the green slice represent species of bacteria that are pathogenic.  And in fact, when Dr Grace combed over my data she identified many pathogens that were likely wreaking havoc on my entire system.  Grace said if I weren’t living such an otherwise healthy lifestyle, these massive perturbations would be showing up as much bigger problems.  We embarked on a 30 day intervention that she refers to as the “Weed, seed and Feed” approach.

The intention was to kill the pathogenic types (weed-herbal liver detox). At the same time, we needed to seed the good types with specific probiotics, and feed them with the specific fibers.  In short it worked. Enjoy the data below.

Also, if you read my first post in this series, Poop: How to Create a Good Poop you will better understand my rationale and motivation for trying out this biohack. To avoid redundancy, I will not repeat the details in this post.


Screen Shot 2015-04-14 at 7.00.53 PMScreen Shot 2015-04-14 at 7.00.09 PM


First off, I want to bring your attention to how my sample now closely resembles the “all samples” data.  You can take what you want from that data point, but I would argue that not being aberrant is good in this case.  Especially because of the shift in the “pathogenic” and “good” Phylum categories. That is the benefit of testing with Ubiome.  You get to compare your data with others to see how you stack up.

Bacteroidetes went up from 8.11% to 23.7%.  That is a 2.9x increase.  Subsequently the Proteobacteria dropped from 18.1% to 4.67% that is a 3.87x reduction.  These two categories stood out the most to me, but delineated further some pronounced changes are worth mentioning.

Dr Grace identified the following bacteria strains as pathogenic and tracked the change pre and post intervention.  The specific implications of shifting these are not yet clear, below I will expound on my qualitative observations during the intervention.

Screen Shot 2015-04-14 at 7.20.24 PM

The two highest values were virtuality eliminated.

Through her extensive research on the topic, Grace has identified what she refers to as the “lean core.”  Here are the fold changes:

Christensenellaceae: ** INCREASED 20-FOLD% to 0.1156
Actinobacteria: (contains Bifido)****** DOUBLED to %1.6265
Verrucomicrobiales: (contains AKk)****  INCREASED FROM ZERO TO A DETECTABLE %0.0011
Akkermansia: %0.0000
Christensenella: %0.0000
Bifidobacterium longum: ****** INCREASED 15-FOLD to %0.0395
Bifidobacterium breve:%0.0011
Bifidobacterium bifidum: %0.0176
Bacteroides vulgatus:  *** INCREASED FROM ZERO to %0.0128
If that all looks like a bunch of Russian to you, you are not alone.  It’s over my head too.
(If you are curious about what all this means and want to know how some of this stuff could affect you, I suggest reading Dr Grace’s blog here.  It’s pretty “sciency”, but if you are into that kind of thing it’s pretty cutting edge in my opinion.)
The bottom line is increases in those strains are a good thing and that happened to me as a result of the protocol I was on.  To sum it up from a data perspective, needless to say there were some massive shifts.  But did the protocol work? Well, yes and no.  That brings me to my qualitative observations on my experience during the 30 day protocol.
For a 10% Ubiome discount use my referral link


 My hypothesis going into this intervention was that food sensitivities I had were derived from a downstream problem with protein digestion in my gut, not genetically pre-ordained food sensitivities or autoimmune issues.  And that the inadequacies in digestion were leading to intestinal permeability, which in turn was showing up on my skin as acne sores.
One day I hope to occasionally enjoy foods I have been avoiding (beer, donuts, pizza, various gluten items) without having an adverse reaction in my skin.  I’m riding a presumption that I am not fundamentally broken or perpetually broken, rather I have compromised resilience, therefor can’t tolerate these relatively hard to digest products.  Please note that this premise is essentially made up by me.  It was entirely possible going in that my symptoms were not connected to what this intervention would/could address. Put differently, the cause of the problem is not known. Even if this intervention was effective, it might not fix the issue.
Below are the the pre and post intervention photos of my back (this is where most of my blemishes occur.) As I am reviewing these photos, one thing that stands out is my skin doesn’t look that bad. I think it feels worse than it looks.  So you might be saying to yourself, what is all the fuss about?  I believe it’s important to pay attention to small symptoms and try to address them before they balloon into bigger problems in the distant future.  Also, I want clear skin because I am relatively vain. The sores hurt and they are annoying!
If you can see past the lighting variance (I did not turn into a lobster in the second photo), you’ll notice the blemishes are gone and have healed up.  But this is not exactly what I was measuring.  The primary measure I was looking for was how my skin would respond to subsequent reintroductions to reactive foods post intervention. I’m sorry to say it didn’t really hold up.  My reactions were less pronounced, but they subsisted when I reintroduced problem foods.  I might need to be on the protocol longer to become more resilient.
Pre intervention upper
Pre intervention
Post intervention upper
Post intervention



Despite the fact that my resilience is not yet high enough to handle problem foods, I have many unsuspected positive results to report.


First and best is that my sleep has significantly improved.  I have never had deeper sleep.  This started to shift almost immediately and during the trial continued to improve.  Honestly, I didn’t know how poorly I slept until it improved.  Of course this led to improved energy and mental acuity.


I also noticed I was rarely hungry.  If you know me I hate being hungry and find it a nuisance. I would rather eat when it’s convenient for me rather than at the whim of my stomach. In the past, I have struggled with being hungry all the time.  I can see how this would come in handy for a person trying to eat less food in order to lose weight.


Another standout change during this trial is that my knee pain has vanished.  In fact, I finished a trail half marathon with copious downhills and experienced no knee pain days following.  This is likely due to other factors like increased yoga, epson salt baths and changes in my training. I did drastically increase my workout volume during this protocol and that has led to problems in the past.  Who knows?


Going back to the skin issue, it did improve during the intervention.  About two weeks out from the finish I also removed dairy from my diet and that seemed to help.  Of course we can’t forget the poop.  I became very regular in terms of time and consistency.  In other words, I created a better poop (no photos included sorry)

There you have it.  I consider this a very successful intervention.  I had a lot of fun doing the protocols and reporting the results.  If you have any major problems I know grace takes virtual clients also, here are a couple products* I used that could get you started:


*Full disclosure, if you buy the products from the links here I get a tiny portion of the revenues.  I wouldn’t endorse something I did not use.

For a 10% Ubiome discount use my referral link

Here are Dr. Grace’s notes and observations from the trial:

Eli’s Wonderful Gut Results

 Dramatic shifts in the leading causes of dysbiosis occurred during the n=1 self experiment. I believe these tie in with the improvements in sleep, mood, athletic performance, and burning body fat. Inflammation dampens our fat burning even for an elite athlete like Eli. He noticed a significant reduction in body fat in this short period. Our brains are affected by opportunistic gut pathogens — they hijack our mind and moods. They control our behavior. Many opportunistic pathogens such as the ones in the group Gammaproteobacteria enjoy simple carbohydrates and sugar. If we feed them, then they flourish and invade. Our best defenses are prudent diets and optimal gut health where our symbiotic commensals are in charge. I call these the ancestral lean core because they manage our metabolism from gut-brain axis. By reducing pathogens through colonization resistance and filling in all available gut ecosystem niches, they minimize potential invasions from all the opportunists that we encounter in our daily lives.

The best defenses are the gut ninjas: Bifidobacteria longum and Akkermansia. They line our intestines from head to toe and we are born with them from mom within hours and they continue protecting us until we die. Antibiotics and C sections unfortunately eradicate these important peace-keeping fighters (Mueller et al, J of International Obesity 2014). We are living in a high tech and pharmaceutical world, however, fortunately we have cutting edge technology like stool testing from uBiome to illuminate the characters and their relative abundance in our gut ecosystems!

The probiotics that Eli appear to have seeded at the genera level at epic and massive levels. His results are not atypical and hopefully he will continue to see anchoring of these vital protectors of our health and longevity. Low gut diversity is associated nearly all post-industrial disorders and poor health. Eli’s diversity has sky rocketed from 63 (identified genera) to 105! The number of orders almost tripled from 22 to 57 orders. Many groups that appeared wiped out into extinction (Verrucomicrobiales) were resurrected like Lazarus from the dead. I am certain two vital gut occupants will make a come back on the next uBiome: Akkermansia and Bifidobacteria longum.

Most Impressive to Me

What I am most impressed with regarding Eli’s progress are the below improvements in peace-keeping symbionts. Many were extinct (likely from antibiotics, diet, etc). Each of these play roles that maintain our metabolism and manage uncontrolled inflammation. Reductions of these genera are all associated with premature aging, obesity, diabetes, digestive disorders, depression and suboptimal cognition. Faecalibacterium are like the cheetahs on the savannah ecosystem. They not only produce butyrate which fuels our colon cells, they control the populations of bottom level feeders and opportunistic animals which may cause ecosystem damage when they run amok. In the human gut, Faecalibacterium are identified as one of the most anti-inflammatory commensal species (Sokol et al, PNAS 2008). Its favorite foods are pectin, soluble fiber, diverse non-starchy plant fiber, whole gluten-free grains, legumes, psyllium seed husk, arabinogalactan, inulin and oligosaccharides (onions, beans, lentils, grains) (Grootaert et al, FEMS 2008). And a diverse and gut synergizing bionic fiber!

Faecalibacterium: 60% increased from 7.4407% to 11.6026%

Christensenellaceae: INCREASED 20-FOLD to 0.1156%

Actinobacteria: (contains Bifido) 200% increased to 1.6265%

Verrucomicrobiales: (contains Akkermansia) INCREASED FROM ZERO TO A DETECTABLE 0.0011%

Bacteroides vulgatus:  *** INCREASED FROM ZERO to 0.0128%

For a 10% Ubiome discount use my referral link

12 thoughts on “Ubiome Post Intervention Data

  1. Congratulations on the big improvement!

    I wonder how “normal” that first sample was. For example, did you by any chance go camping, travel internationally, eat/do something unusual the week or two beforehand? Such unusually high Proteobacteria in the first sample might have been an aberration.


    1. That’s a great question. I think the initial sample was a pretty good representation of my state at the time. The only varience was the weekend preceeding my ititial sample was the super bowl. On that weekend I had some alcohol and many simple sugars. But I didn’t submit my sample until the following Thursday. Who knows? What I can say is that in the time post my initial test, I significantly changed many aspects of my diet. In addition to that, I had a pretty unfavorable diet for the gut. Low fiber, high fat, high simple sugar cyclically, no probiotics, coffee most days. I was not very surprised to see such a big shift.


    1. Definitely not. If you read the post and the preceding posts in the series, you will see that the shift likely occurred because of the combination of probiotics, resistant starch and the liver support regimen.


  2. Hey Elijah. Congrats on your success. If you don’t mind me asking, how did you time the botanicals you took? (with a meal or on an empty stomach; with/away from probiotics; etc.)


    1. The botanicals were split into two doses. The goal was to take them with meals but away from probiotics. Typically what I did was take the first dose with lunch and the second with dinner. I would take to probiotics in the morning.


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