Hacking your gut: Changes in bacterial functions

In one of my previous blogs I went over some of the changes I’ve seen in my Ubiome test results since applying a different set of principles.  You can find that one here.  Keep in mind that my diet and exercise have been pretty consistent throughout.  The primary changes between my first 3 tests and most recent are:

  • Regular consumption of a few nutrients/supplements
  • Removal of supplemental fiber
  • I also dropped an antibiotic bomb on my microbiome and tested before and after to see what happened

The results from my last blog showed that I:

  • Increased my diversity
  • Completely flipped my Firmicutes:Bacteroidetes ratio from 4.9:1 to 0.6:1
  • Saw a drop in Clostridia
  • Found a new protective guy in my gut called Christensenella
  • Restored my Bacilli levels to pre-antibiotic levels

Of course, diversity is only a good thing if you have a diverse set of bacteria that do positive things.  If I have a diverse set of pathogens, this wouldn’t be a good thing.  So my next step is to look at the functions going on in my new microbiome and see if these new functions are protective.

Another thing I can do is take a look at these functions as markers for improvement.  Some of the mechanisms I’m manipulating will change microbial functions and show that I’m doing what I think I’m doing.

Before we get to the fun, it’s important to note that I’ve also done blood tests to get a look under the hood.  My primary goal is to be healthy, and I’ve done a lipid panel and A1c testing during uber-strict Paleo dieting and what I do now.  The results speak for themselves:

blood-dataOverall, I’m happy with these results.  I’m regularly eating bread, eating pizza or other high calorie foods on weekends and drinking craft beer.  While my hemoglobin A1c went up, it’s still within a healthy range and I don’t feel like I’m starving myself or being restrictive.  This is great because 23andme shows that I have a high risk of Type 2 diabetes, obesity, and cardiovascular disease.  Part of the change in hemoglobin A1c may improve by reintroducing supplemental fiber.  I think I’ll do that after my next Ubiome test.

Now that we’ve got that out of the way, let’s dig in to the changes in microbial functions in my new microbiome.

Changes in lipid metabolism


First up on our look at the changes in bacterial function in my microbiome is lipid metabolism.  The old data is on the left and the new data is on the right.  I saw huge increases in:

  • Steroid biosynthesis
  • alpha-Linolenic acid(ALA) metabolism
  • Sphingolipid metabolism
  • Arachidonic acid(AA) metabolism

One of the problems with my data is that the largest change came in steroid hormone biosynthesis.  This function went from .02x when compared to all Ubiome samples to 2.66x.  That’s a huge increase, but it’s also not specific.

Am I making more corticosteroids or more sex steroids?  If it’s testosterone I’ll take it, my testosterone is at the bottom of the reference range for my age.  But, if it’s DHT I’ll pass.  More corticosteroids could be good or bad.  The increase in ALA metabolism kind of hints that it could be more towards an increase in androgens.  But, I don’t know for sure.

The other changes in lipid metabolism are pretty interesting.  I consider AA and ALA metabolism to be indicators of a change in dietary composition, but I didn’t change the types of fat I consume.  I eat mostly saturated fat which shouldn’t change AA or ALA metabolism.  Looking at them in conjunction with the change in sphingolipid metabolism leads me to believe a positive change in bile content.

The 3 primary components of bile are bile acids, bilirubin, and phospholipids.  An increase in phospholipids in bile is protective against bile acid induced injury.  Since all 3 of these lipids are important components of cell membranes, an increase in their metabolism could signal cellular repair in the gut.

My thought process here is that the contents of bile are not just meant to help digest and absorb fats.  These 3 components of bile help regulate the GI environment.

  • Bile acids are antimicrobial and help regulate the integrity of the intestinal barrier.
  • Bilirubin functions as a fat soluble antioxidant to help repair damaged cell membranes.
  • Phospholipids provide building blocks to help repair cell membranes.

Each of these is cycling through my gut 7-10 times per day, so there’s a good chance they’re changing things.  I don’t know for sure this is what’s happening, but I’ll take it.

Changes in secondary metabolite degradation


Next up is secondary metabolite degradation.  Again, old data on the left, new data on the right.  Most of the secondary metabolites they look for are used to degrade plastics or pesticides.  I don’t think I can pull much out of this information.  Greater plastic and pesticide degradation in the GI tract could be from ingesting more in what I eat, or greater dumping of stored toxins in the bile.  I don’t think I’m ingesting more but I have no way of figuring that out.

One interesting change to note is the change in cytochrome P450(CYP450) metabolism. Both “Metabolism of xenobiotics by cytochrome P450” and “Drug metabolism – cytochrome P450” were too far down the list to make the chart in my first tests.  But, they were .56x and .54x, respectively.  They both almost tripled in the second test.

One of my primary goals was to induce CYP450 in the cells of my GI tract.  This is important because they inhibit inflammation and improve intestinal barrier integrity.  I don’t know that the increase in bacterial CYP450 indicates an increase in my cellular CYP450 enzymes.  At the very least it indicates that I’m challenging the bacteria in my gut in some way.

Secondary metabolite synthesis


Of the results in this newest Ubiome test, the results for secondary metabolite synthesis give the greatest sign that there are some positive things going on.  The first obvious change is the humongous increase in “Stilbenoid, diarylheptanoid, and gingerol biosynthesis”.  These processes increased from .05x of “All samples” to 5.69x.  This is a 100x increase.  But what are they?

These three classes of compounds are antioxidants produced by plants and bacteria that have beneficial effects in humans.  Examples of well-known plant-based compounds that belong to these groups are:

  • Stilbenoids-Resveratrol from grapes and pterostilbene from blueberries
  • Diarylheptanoids-Curcumin from turmeric
  • Gingerol-Active component in ginger

All 3 of these compounds have strong anti-cancer effects and affect inflammation and/or inflammatory diseases.  Having a bacterial factory producing them in my gut is definitely a welcome effect.  Other notable changes in plant-based antioxidants include an increase from .26x to .44x in “Flavonoid biosynthesis” and an increase from 1.49x to 1.76x in “Flavone and flavonol biosynthesis”.

Another large change in the data involves “Penicillin and cephalosporin biosynthesis”.  This increased from .48x when compared to “All samples” to 1.8x.  Streptomycin also increased from .92x of “All samples”to 1.19x.  All 3 of these are antibiotics used by bacteria to fight other bacteria/fungi.  There’s no doubt that these increases are having an effect on my microbiome.  The question is whether it’s good or not.  Since my diversity is improving, I’m guessing it’s good but the jury is still out on this one.

Vitamin metabolism


My initial results looking at vitamin metabolism were pretty unremarkable.  Fast forward to my most current results and we see some big changes.  First, lipoic acid metabolism increased from .33x of “All samples” to 2.12x.  This is an almost 600% increase.  Given that alpha-lipoic acid is an antioxidant that can work in water- and fat-based tissues, this is great.

Lipoic acid is also a co-factor that works with thiamine to help produce energy and reducing equivalents from carbohydrates.  It’s likely through these 2 pathways that alpha-lipoic acid inhibits tumor cells(1).

Cancer cells are less efficient at creating energy from glucose which causes them to make lactic acid.  Alpha-lipoic acid works with thiamine to make sure that this process is more efficient, decreasing lactic acid.  I definitely want a good amount of this stuff in my gut.

Retinol metabolism is another pretty big change I saw between tests.  It went from .58x compared to “All samples” to 1.62x.  In bacteria, this pathway starts with 9-cis retinol, a form of vitamin A.  This was actually one of the things I was trying to improve for 2 reasons:

  1. I have a polymorphism that prevents me from converting plant-based vitamin A to the usable form
  2. This form of vitamin A is the ligand for the retinoid X receptor(RXR).

I’ll definitely be talking about that one in detail in future blogs.  Let’s just say that RXR makes other cellular receptors work better.  This is probably one of the things increasing steroid hormone biosynthesis and improving my overall digestive health.  In theory, it should reduce gut inflammation and improve “leaky gut”.

The final major change in this category is in “Ubiquinone and other terpenoid-quinone biosynthesis”.  This category indicates that my bacteria were creating CoQ10 and/or vitamin K metabolites at 3x the previous level.  Both of these nutrients play a large role in energy generation and antioxidant defense.

Just like alpha-lipoic acid, both are fat soluble which makes them better suited to repair of cell membranes.  While glutathione gets crowned the king of antioxidants, it’s greater solubility in water makes it more suited to repairing proteins.


Thus far, I think the changes I’ve implemented have improved my microbiome and the health of my gut.  I feel great and my digestion has improved.  Generally my digestion is pretty good, but I do love craft beer and tend to get issues on weekends when I drink it.  Before my stools after the weekend would float and were lighter in color, potentially indicating fat malabsorption.  Now, my stools are better formed, they tend to sink, and the color is pretty stable.

My Ubiome results are also pretty promising:

  • My diversity increased
  • My Firmicutes:Bacteroidetes ratio improved
  • My Bacilli levels recovered to pre-antibiotic levels
  • And I saw increased synthesis of many antioxidants

Other changes in lipid and vitamin metabolism may indicate improvements, but they could also indicate increased intake.

One of the drawbacks of Ubiome testing is that it’s overly sensitive to changes in diet.  In my first 3 tests, bacteria and bacterial functions didn’t fluctuate that much.  The big change seen on my last test may be due to my change in protocol, but it could also just be an aberration in the data.  I recently sent in my last test and will blog about it when I get those results back.  I’m hoping to confirm the changes were due to my protocol, but you’ll have to stay tune to find out.

Next up is a comprehensive blog on what I did and how I used my 23andme results to personalize my approach.  That one’s going to be private and you can access it by requesting to join here.

For the previous blog in this series, click here

For the 3rd and final part, click here

Interested in improving your digestion, protecting your digestion while taking pharmaceutical drugs, or deciphering your digestion woes ?  Shoot me an email by clicking the “contact” page on the menu at the top and we can see if I can help. 


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