I recently participated in the pilot test for Ubiome‘s new clinical microbiome test.  I had no overt stomach issues (although I do now, long story…).  I was doing this mainly to assess the health of my gut bacteria.  They took 900 healthy people and established a reference range (the science on the gut microbiota is still nascent).  Any bacteria outside of the 99th percentile was considered abnormal.  I had four abnormal bacteria: Butyrivibrio crossotus, Dialister invisus, Lactobacillus, and Ruminococcus albus.  All four were on the low side.

Lactobacillus is found in yogurt, so I am consuming more of that.  They recommended lactobacillus plantarum for Ruminococcus albus, and a lower carb diet to increase Butyrivibrio crossotus.  At this point I am doing neither of the last two recommendations.  But I can’t get enough yogurt…

Attached is the report:

uBiome SmartGut™ Report – 2178228b-6fee-47ac-bdeb-2bd898194b46


Nuts for Nuts

I recently came across a meta-analysis regarding nut consumption and health outcomes.  Meta-analyses are generally far better regarded than several studies alone, as they look for general trends across many studies.  This includes looking for inconsistencies in data, conflicts of interest, or how well the study’s authors controlled for variables.

Daily nut consumption was shown to be associated with a 22% reduced risk of all-cause mortality, 30% reduced likelihood of coronary heart disease (when arteries become hardened and narrowed), and a 40% reduced risk of DYING from diabetes.

So what were the key points, and how might it relate to acne?  First of all, 20 grams of nuts per day maximizes benefit.  Anything above that provides no further benefit.  This amounts to a handful, or a little less (I have big hands, just like Donald Trump).  I personally got out my gram-scale and weighed nuts, just to get a general idea as to how much 20 grams is.  Brazil nuts weighed about 3 ounces, so it would take 7 per day to achieve 20 grams.  Walnuts were heavier than I had assumed, as it was about half a handful of walnuts to reach 20 grams.

According to the analysis, nuts are helpful because they are “high in fibre, magnesium, and polyunsaturated fats”.  The study’s author also notes that “Some nuts, particularly walnuts and pecan nuts are also high in antioxidants, which can fight oxidative stress and possibly reduce cancer risk. Even though nuts are quite high in fat, they are also high in fibre and protein, and there is some evidence that suggests nuts might actually reduce your risk of obesity over time.”

Looking at biomarkers for acne patients, they tend to be deficient in certain polyunsaturated fats and various antioxidants.  It seems prudent to include a handful of nuts in your daily diet.  I personally eat only 2 meals per day and then have a handful of nuts mid-afternoon.  This has worked out well for me, as I save time and money.  I also feel fine doing it.


Reversing the damage of Antibiotics on your Gut Microbiota

People with acne are intimately familiar with gut microbiota.  Having severe or moderate acne probably means you have cycled through tetracycline, minocycline, Azythromycin, and doxcycline, among others (these are the ones I have used)…

Unfortunately for us, research in the past decade is indicating that these bacteria are pretty damn important for our systemic health.  I have gone down the rabbit hole of gut testing–I have already used Ubiome (many times), American Gut (once), and the more comprehensive Genova Stool Test (results already posted).  I am not going to fool you into thinking that these are diagnostic or incredibly actionable at this point.  Most of it has been interesting, but it is still somewhat preliminary.  Have I been able to ‘target’ and change these things?  Not really.  I have been messing around with DIY fecal transplants, which I will do a blog post about soon (yes, fecal transplants are a thing but the FDA only allows it to be performed clinically for a very small number of conditions, unfortunately).

As a general rule of thumb, I always participate in research.  I recently participated in Ubiome’s mental health study.  I was very impressed and look forward to seeing the results.  I also received a free gut kit from it.

Another company that I have been really impressed with, and testing with of recently, is The Biocollective.  Martha Carlin, the CEO is awesome.  Her TED talk about the gut microbiota of Parkinson’s patients is here:

Martha is  dead set on figuring out how the gut microbiome interacts with human health.  To get your gut sequenced, check out the website.  You can get the basic bird’s eye view of your gut bacteria done for free.  To get fungi, viruses, parasites, and bacteria checked, you can use the code word CAND50 for 50% off–this brings the standard kit’s price to $275– a good deal in this world.  And I am sure the price will drop in coming years as the price of sequencing continues to drop.  So if you take a shit–get tested.  It isn’t tough, the data benefits us all as we learn about us–the super-organisms that we are.

Acne Revolution and Microbiome Insights

Ben at Acne Revolution has been doing some interesting work into the microbiome of people with acne and other conditions. He was recently featured on the UBIOME blog here.  I encourage you to check out his blog and perhaps perform your own experiments through Ubiome, which is revolutionizing Microbiome research. (also for redditors, /r/microbiome has a lot of good links on the subject)

Ubiome is very affordable at $89 per stool kit.  It is not as comprehensive and diagnostic as the Genova stool analysis, but it will do much more to move research in that area forward.

I am very interested in individual bacteria such as Akkermansia Mucinophilia (which I had very low levels of).  Akkermansia Mucinophilia has been show to play an important role in intestinal health and in preventing diabetes and obesity.  For those with mental health conditions, microbiome research will hopefully revolutionize psychiatry.

 Here is Ben’s post reviewing some of the insights that I have found.

The more people we can get doing this sort of thing, the better.

Also in other news, for Arizonan readers, self testing just became much easier and cheaper through Theranos.  This should spread throughout the country quickly, making self-testing much more affordable and easier.

Stool Analysis: A Brave New World

IMG_20141211_094833282 (2)IMG_20141211_094859068 (2) IMG_20141209_075623844 IMG_20141209_075615973 IMG_20141209_075607453

Also not shown: Negative for Clostridium Dificile, H. Pylori, and a few other bacterial infections.

Fortune Magazine says that 2015 will be the ‘Year of the Microbiome’ in their forecast for business trends.  I believe this test should be common practice for most problems, given my experience with it.

I had low levels of microbial diversity.  I am somewhat confused as to why that is.  Was my probiotic actually full of live culture?  Was I taking a ‘natural’ compound that had strong antibacterial properties?  I am not sure and am working to figure this out.

Another interesting thing was the low levels of short chain fatty acids, particularly butyrate.  I was completely unaware of short chain fatty acids prior to this test, so it has certainly opened up a new avenue for me.  I was very surprised at how closely correlated butyrate was with allergies and asthma, which may be relevant to some of you.

Fecal short chain fatty acid pattern and allergy in early childhood

High fiber diet may prevent asthma (due to the short chain fatty acid’s immune-modulating properties — fermentable fiber increases short chain fatty acid production)

Interestingly, butyrate resembles sodium valproate in structure.  Valproate is a common drug for bipolar, seizures, migraines, etc.  I think stool analyses for people with these problems could potentially reduce symptoms, or it has potential anyway (note: not a doctor, just documenting my personal experience. Interpret it as you will).  Asthma is associated with an increased risk of bipolar, so maybe this is one of the underlying mechanisms. To add insult to injury for asthmatics, high doses of corticosteroids (prednisone, advair, etc.) further increase that risk.

Relevant to acne, butyrate increases insulin sensitivity (in a mouse model) and positively affects markers of inflammation.

I have since changed my probiotic and have increased my fiber intake, particularly by eating more vegetables(5+ per day). I would imagine one could supplement sodium butyrate to achieve some benefits as well, although I would imagine it wouldn’t confer the same benefits to the colon.

I would be very curious to see other stool analyses and their potential connection to various disease states.

Also, this was on today: Connection made between gut microbiota and Parkinsons

Novel Acne Therapies

If you haven’t figured out by now, this blog is not about having perfect skin.  It is mainly about preventing people from going down the traditional route of acne therapy which is ridiculously expensive and more importantly, can potentially have horrendous health consequences.  Isotretinoin and long-term antibiotic use are amazingly still routinely used for acne, and both can have side effects that can ravage mental health under the right conditions.  The intestinal microbiome is 3-5 pounds and humans have 10x more bacterial cells than human cells.  Arbitrarily taking antibiotics, in the evolutionary sense, makes no sense.

I know someone who developed high levels of HPHPA, a clostridia bacteria that affects dopamine metabolism. They suffered this presumably from taking long-term antibiotics combined with a poor immune system and poor diet.  This website is not here to make you look like Fabio, but to make sure that you don’t head down a much worse road.  I would say mental health but that would be a misnomer.  In the past I have received terrible advice from dermatologists.  One doc said it would be fine if I loaded up on aspirin everyday to reduce acne inflammation.  Aspirin is an interesting drug, but is there not an easier and more sustainable path to achieve the same outcome?

Life can be tough however, and use every tool available to you.  Exercise and diet should be first-line therapy, not third-line.  However there are some compounds that are of interest in regards to healing acne should correcting deficiencies fail.

Metformin: Acne is related to pre-insulin resistance.  Metformin is an interesting drug with potential life-extension application.  If acne is associated with elevated cumulative insulin levels, metformin may ease the burden.  This could be particularly helpful if markers for diabetes are particularly high (fasting insulin, Hemoglobin A1C).

Anti-inflammatories: If acne is an inflammatory disease, then anti-inflammatory drugs should work.  I wouldn’t recommend this, but it is an option. Adequate vitamin D levels would also be another route for potentially reducing inflammation.  It is correlated with lower levels of inflammation.

Anti-anxiety/stress options: Adaptogenic herbs are interesting and typically not used clinically.  They are understudied, can have side effects, but have a lot of potential as well.  Acne is correlated with higher levels of cortisol, the stress hormone.  One mechanism I can see causing a problem here is that elevated cortisol tends to break down collagen which is important for skin barrier function (not to mention muscle and connective tissue as well).  Low dose anti-depressants could be beneficial in some perhaps.  Glycine would be very beneficial as well, particularly in a gelatin mixture.  This would hit both skin/joint health and stress.  Vitamin C is important, particularly in those who have an increased demand due to elevated cortisol levels. Vitamin C is crucial for collagen and thus skin health. Current demand for vitamin C can be measured by urinary vitamin C (if low necessitates more vitamin C).

Novel compounds: Cocoa

Increased intake of carotenoids (spirulina springs to mind)


Reddit/foodnerds is an interesting study dump– I recommend subscribing.

Anyway those are just a few thoughts.  Be pragmatic.  I am not against pharmaceuticals in the least, but I do believe that most of the RX meds that dermatologists rely on are unnecessary 80% of the time.  I also wanted to reiterate that this blog is not designed for the person who only has 2 or 3 pimples. It is designed for the person who has moderate to severe acne and is headed down a bad road ‘mentally’.   I can relate to the latter and not the former.    At the end of the day I think there are very few problems that education can’t solve.  Acne and health are no exception.

Acne and Inflammatory Markers



I just wanted to get this out there.  Acne does not seem to be related to inflammatory markers, at leas the ones presented here.  A suspicion I have is that acne is related to interleukin 1beta, although that is not measured on this test.

From my findings acne seems to be related much more to insulin resistance instead of markers for heart disease. 

On my next post I will document potential integrative pharmaceuticals for acne (life is short and while foods are the basis for health, not all problems can be overcome in a timely fashion with kale and coconut oil).  I will also upload another test, but the internet is so damn slow right now…

Also HDL Labs has a great basic panel and if anyone is looking for blood testing they should consider their basic panel.

Acne and Intestinal Dysbiosis (Urinary Organic Acid Test)

Organic Acid Nameless

Above is the urinary organic acid test.  Urinary organic acids are measures of metabolites of intestinal bacteria that are released into the bloodstream.  There are several other urinary markers as well, including urinary neurotransmitter metabolites.

Relevant to acne, there is a vitamin C deficiency (vitamin C excretion = 0).  Vitamin C is important for collagen formation and skin structure.  Collagen/gelatin supplementation is an interesting avenue for healing acne scars.  Elevated cortisol (the stress hormone) causes a breakdown of collagen into amino acids, thus leading to a loss of skin structure.

There are markers for bacterial dysbiosis.  Arabinose is elevated, which is a marker for yeast overgrowth.  Acne patients tend to have dysbiosis.  This may be due to the traditional route of using antibiotics for acne (very short-sighted approach!), or it may have something to do with lack of essential fatty acids allowing for intestinal permeability (which wouldn’t inherently cause bacterial overgrowth AFAIK).  Either way antibiotics should not be prescribed anymore for acne.  If you want to go the antibacterial route, use coconut oil for caprylic acid and lauric acid, or ideally get your fatty acid profile done and get them into optimal zones, and the problem may resolve itself.

I used to look forward to not having acne due to this:, but now I realize how silly that is when you could simply take coconut oil and over time reap the benefits of the systemic effects as well.  A lot of these researchers are more interested in making $$ by formulating patentable compounds, so keep that in mind when going through research articles and constantly try to figure out the integrative approach.

Also, as far as neurotransmitters go, I had high levels of dopamine compared to norepinephrine.  Norepinephrine is the downstream metabolite of dopamine (by the enzyme dopamine decarboxylase).  Copper is needed for this conversion.  I had low plasma copper levels, due to long-term zinc supplementation.  Zinc in high doses is recommended by many acne sites and practitioners, but be vigilant to not overdo it in either direction.  Keep a 15 mg to 1 mg Zinc to copper ratio through supplements AND diet.  Ideally, TEST TEST TEST.  That is the best way to know what your levels are and avoid problems downstream.

Acne and Hormones

Soon I will be compiling various tests on hormones and their correlation with acne. Some are already on various posts. Cliffs notes until then: Positive correlation between Acne and testosterone, cortisol (only tested once, so nothing to compare it to), DHT. Lowering these hormones (other than elevated cortisol) seems unwise in regards to holistic health, especially in males. No correlation in acne and fasting blood glucose, estrogen, or IGF-1. Likely a correlation between acne and Oral Glucose Tolerance Test.
Also I will post complete hair mineral analysis as well as urinary organic acids (have to get another one from the lab). No major problems with urinary organic acids, but depleted urinary vitamin C as well as slightly elevated markers for candida and a few other ‘bad’ intestinal flora. Seems wise to take a probiotic, especially if you have run courses of antibiotics for acne in the past.
Hold me to getting these posts up!

Acne, Fatty Acids, AND Amino Acids

Test Date: February 2014

# of Lesions: 10

Diet/Supplements/Drugs: Lower Carb, Paleo-ish diet, with milk/Spirulina 50 mg/day for past 6 months (around 30-60 mg GLA per day), vitamin D, Aged Garlic Extract, Magnesium citrate, b12 1 mg)










Even after 6 months of supplementation of GLA the GLA, and more importantly DGLA, were on the very low side. DGLA is the precursor to anti-inflammatory prostaglandin E1, and can also be converted into arachidonic acid. There are many checks and balances when it comes to fatty acid metabolism.

The interesting thing to me on this test was the taurine deficiency. All of my fatty acids trended low, and lo and behold taurine is a necessary constituent of bile, which is necessary to break down fats and fat-soluble vitamins (vitamins A, D, E, and K). 1 gram 3x per day is standard dosing, preferably before meals to increase fat absorption.

Taurine is found in seafood and meat, and to synthesize it naturally the body needs the amino acids cysteine and methionine, plus the activated form of vitamin B6, p5p.
Taurine regulates blood sugar as well, and decreases inflammation in obese people. It is an interesting amino acid.

The high Linoleic acid: dihomo-gamma-linolenic acid ratio, even after long term low-dose supplementation of GLA seems to indicate that Delta-6-desaturase enzyme is not converting Linoleic acid to Gamma Linolenic Acid effectively. For this enzyme to function properly the vitamins and minerals zinc, b6, C, and magnesium need to be present. There could also be genetic aspects for the dysfunction.

Gamma Tocopherol was also on the low side. Long term supplementation of Alpha-tocopherol can deplete gamma tocopherol, so supplementing mixed tocopherols or ensuring vitamin E from natural sources is wise.

The copper is low, which in all likelihood is from excessive zinc supplementation. Both are relevant to the acne discussion, and I would recommend that you personally check your plasma levels of both, or do a hair mineral analysis to get personalized recommendations. Rule of thumb is 15 mg zinc per 1 mg of copper.