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
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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.
PRE INTERVENTION DATA
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.
POST INTERVENTION DATA!
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.
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:
UNINTENDED POSITIVE SIDE EFFECTS:
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.
DECREASED SENSATION OF HUNGER
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.
KNEE PAIN GONE
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?
SKIN AND POOP
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%
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12 thoughts on “Ubiome Post Intervention Data”
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.
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.
Awesome change. I am impressed.
Is this all result of resistant starch ‘only’?
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.
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.)
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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