I Have a Fucked Up Gut

I’ve never cursed in a blog title before. It feels good – I should do it more often.  This is also the first time I’ve posted from my phone. Sometimes I just need to express myself, I guess.

I’m at a loss with my gut. Something from my “safe ” list (probably my apple a day) decided to feed my fucked up gut pathogens and make me depressed.  Unsure of how to fix this, I’ve been trying to eat some fermented food (sauerkraut) over the past 2 days. Not going well either. I’ve started tracking heart rate variability (details to come in a future post) and it indicates increased sympathetic nervous system activity and decreased heart rate variability over the last 2 days.

A zero-carb diet is sounding better and better all the time. I miss feeling good.

Methodical Progress and MTHFR

I’ve been gradually adding in foods to see what I do and don’t tolerate.  I’ve had a few bumps along the way, specifically when I ate some nightshades. The following foods seem to be thumbs up so far:

  • Meat (all kinds)
  • Eggs
  • Coconut (all forms seem to be ok – I’ve had coconut oil, coconut butter, coconut milk, and coconut aminos)
  • Spinach
  • Mushrooms
  • Macadamia nuts
  • Carrots
  • Apples

I’ve decided to start adding whole fruit into my diet again, starting with having one apple every day for the last 4 days.  I wasn’t sure if the fiber in the apple was going to cause me problems so I’m starting slow (and so far, so good).  My plan is to gradually add and see at what point my blood sugar and/or mood start to struggle.  Watermelon is the next one to try.  So why am I adding sugary fruit?  Well, I’ve been noticing loose strands of hair on my shoulders and and shirt a lot lately – I’m not sure if I’m losing hair because my thyroid is suffering (my high reverse T3 would suggest that this is indeed the case) or perhaps because of the physical stress associated with losing weight.  In any case I would like to test the hypothesis asserted by Ray Peat that diabetes is not caused by sugar – rather, it’s caused by high PUFA consumption.  As I’ve been losing weight I’ve been presumably detoxifying some of the stored PUFA, and I’ve been avoiding it in my diet.  If what Meme wrote was true, then I should be able to tolerate more sugar and eventually be CURED of diabetes.  Wouldn’t that be something?  Now, that would be worth blogging about.

On another topic, I’ve been learning more and more about MTHFR mutations and their impact on health.  According to 23 and me I’m heterozygous for the MTHFR C667T mutation (as is my daughter) while my husband is homozygous. I’ve been taking methylated B vitamins as part of my Nourish Balance Thrive protocol, but I wanted to see what would happen if I started them on something similar.  Here’s what we’ve found so far:

  • Husband (homozygous for MTHFR C667T) – Started him on Methylfolate and he got really mellow.  He described it as his adrenaline being turned off.  I added Methyl B12 and he got irritable for several days in a row (unheard of for him).  I was starting to take it personally, and then I remembered reading that people who also have a COMT mutation (he does) don’t always tolerate methyl B12 well.  So then I swapped that out for hydroxy B12, and he’s doing well on this.  I’m interested to have some basic testing done in a month or two and see if it’s affecting anything for the better.
  • Daughter (5 years old) (heterozygous for MTHFR C667T) – Started her on a methylfolate and methyl B12 lozenge.  She was doing great on this.  She became calmer and less interested in television, more interested in playing quietly.  I always knew she wasn’t an “easy” kid, but now I think this mutation may have been causing her to run a little hyperactive.  Well, this went so well that I tried to add in a multivitamin that also had methyl folate and b12, in addition to some other things she may need.  She started having nightmares almost every night.  Huh? I checked the label and the form of B6 in the multivitamin is Pyroxidine Hydrochloride – not the P5P (bioactive) form of B6.  I remember hearing/reading that B6 can be related to dream recall and too much or the wrong form can cause nightmares.  So we stopped the multi and she’s back to sleeping through the night most nights again.  Still continuing on with the folate/b12 lozenge.  I’d like to find a kid’s chewable vitamin that has the P5P form of B6, but so far I haven’t found one.  B6 doesn’t get as much press as the folate and B12, I guess.  Or maybe it tastes bad so they don’t put it in chewable vitamins.

Here’s another twist on the genetic whirlwind I’ve been researching.  I put my genetic data into Nutrahacker, which is free for some reports, including one that tells you which substances/supplements to use and which to avoid, considering your genotype. I found out that B2 in its active form (Riboflavin 5′-Phosphate, or R5P) can be helpful for lowering blood pressure in people with my genetic profile.  So I got some and have been trying it for the last few days.  There’s already some in the multivitamin I take but the supplement by Thorne includes an additional 36mg per day.  Well today, after taking this for 2 or 3 days, my blood pressure dropped from around 136/84 (medicated) to 118/80 (medicated).  Something shaved off almost 20 points from my systolic BP.  Unprecedented.  Hoping its the R5P.  I’d like to stop supporting Big Pharma.  I’d rather support Big Vitamin.


I may have made an interesting discovery about myself.  I think I may be sensitive to nightshades.

Recently I started gaining weight again – not much, just a couple pounds – but it didn’t make sense.  I was in the process of losing weight and my diet seemed to be unchanged calorie-wise, yet the scale started climbing.  I attributed this to the addition of prebiotics, but now I’m not so sure.  It occurred to me that might have something to do with food intolerance. I remembered from back in my floundering-about days hearing this concept in Lyn Genet’s book, The Plan – that one can lose weight easily as long as you aren’t eating things you are sensitive to (the trick being to identify which things those are). I moved on pretty quickly from The Plan at the time because I couldn’t subsist on bird seed and I found her recipes to be annoyingly vague.  However, the idea that prevention of weight loss – or weight gain – could be related to unidentified food intolerance stayed with me.

I started thinking about this again last week after eating a bunch of roasted bell peppers…and then having my shoulders ache for the next couple of hours.  And then doing it again and having my shoulders ache again.  Peppers are in the nightshade family.  I hadn’t given nightshades much thought over the years – I didn’t have much pain (in the joints or otherwise) so I figured they were probably safe for me.  I do remember Jack Kruse saying once that if your HDL cholesterol isn’t over 50 (or was it 60?), “you have no business eating nightshades.”  Hm….my HDL tends to run low.

A week or so ago I decided to limit my diet to only that which I know is absolutely safe for me – foods that have never inhibited weight loss for me – and then add in questionable foods one at a time to distinguish the troublemakers.  Meat, coconut oil, eggs, and a couple of different vegetables (spinach, mushrooms) were on the list to start.  Pretty limited, but I knew it was temporary.  The first addition was macadamia nuts.  That went fine and I saw a loss on the scale the next day.  The next addition was tomatoes (yesterday).  That did not go fine.  My face started getting itchy and breaking out last night, and today the scale is UP a pound.  This, in addition to the shoulder pain following pepper consumption, makes me think maybe I actually do have trouble with nightshades.

So tomatoes, peppers, and eggplant are now off the menu.  I’m interested to see if this makes a difference.

I’ve been reading about Kim’s success with a Zero Carb diet, including significant weight loss and loss of body fat, but also improvements in digestion, mental clarity, reduced fatigue, and on and on.  I think maybe the magic of the zero carb diet lies not in what one IS eating but rather in what they’re NOT eating.  Maybe losing excess body fat is really just a matter of getting certain substances out of the diet so the gut can heal up and big picture healing can begin.

Which brings me to another point – the depression I experienced after eating fibers again – Would this have been a problem if my intestine wasn’t permeable?  I mean, the depression was likely caused by endotoxin – byproducts produced by pathgenic bacteria in the small intestine, which managed to get into the blood stream via gut leakiness.  And how come that’s not healing up?   Dr. Allison Siebecker says the gut can heal in a couple months once the insult is removed.  How come mine hasn’t been healing up?

The cursed nightshade.

Bye bye tomatoes…I’ll miss you.  Eggplant, not so much.  Potatoes…I’ve loved you but we’ve been apart for too long anyway.  I almost forgot about you.

Oh crap, I need to get rid of my vast collection of hot sauces.  Darn it.


Well, my depression and fatigue continued a couple more days.  Also my weight started trending up even though my diet didn’t change.  A glance at the data I keep indicated all of this turned for the worse when I added prebiotic fibers to my world, which suggests I managed to re-grow something (or someone) – some kind of unwelcome visitor in my gut, some type of bacteria or pathogen.  So I decided to take antimicrobials for another couple of weeks to kill whatever I managed to grow with the prebiotic fibers.  I’m about 5 days into that now and feel much better.  In the last 3 days I’ve lost 3 pounds (finally below 190) and the fatigue and weepiness are gone.

My NBT coaches indicate a very low and slow approach to adding fiber might be best.  Honestly I’m not ready to add it back in yet.  That was a pretty aversive experience.  I’m thinking of just adding probiotics for now and gradually – super super gradually – adding in one form of fiber.  I’m talking so gradually that it’s almost imperceptible.  Like you can barely see it on the spoon.

I’m excited about things in my life right now. I’ve been learning biochemistry using Bryan Walsh’s Metabolic Fitness Pro videos – they’re very dense but awesome and not impossible to follow for a lay person like myself.  I also find myself exposed to people who are using the same medical interventions I’m using on myself, but to treat children with autism.  This coincides with the work I do for a living, and has become immensely interesting to me.  I’ve decided to use all of these tools to create resources for parents.  I’m not sure how this is going to look yet, but I’m sure it’s going to be great.  It feels like doors are opening for me.  I could never have taken on a project like this while feeling as sick as I did back in December.

There have been other psychological changes as my health has improved.  I’m much more patient and understanding now.  I have the energy to look people in the eye and listen to them, sensing what they need and giving it to them.  Previously I was in such a dark place that I could barely look up.  Sometimes it was hard to leave the house knowing I’d have to see people.  I was so tired and irritable all the time, I was a toxic burden on society.  It helps me to understand something I’ve always heard and known at some level…people who are behaving badly are in pain.  The badness of their behavior is proportionate in severity to their pain.  Feeling so much better is making me into the person I’ve always seen myself as but couldn’t quite bring myself to be.

This is worth whatever it costs.  If you’re reading this and you’re on the fence about whether you’re worth spending the money, the time, or the effort on, you are.  Just do it.  If not for you, then do it for everyone you encounter.  When you’re sick the world is scary and you react to it in a fearful manner.  When you’re well you can do whatever you’re supposed to be doing and make it better.

Current Plan – 3 Month Review

Well it’s been 3 months since I started following a diet (low-carb paleo) and supplement plan recommended by Amelia and Christopher at Nourish Balance Thrive.


I had a bunch of testing done:

  • Biohealth 205 Adrenal Stress Profile (hormones)
  • Organix Comprehensive Profile (test for nutrient deficiencies, detox pathways, gut issues – an amazing test actually)
  • Biohealth 401 GI Pathogen Screen (gut pathogens)
  • Biohealth 418 H. Pylori Screen (H. Pylori)
  • Genova GI Effects Microbial Profile (gut pathogens)

NBT developed a health plan for me that included a crap-ton of supplements.  It was a little overwhelming at first, but now that I’ve learned more about each of these I can see that each one of them is completely necessary and all are well-supported scientifically.

A couple weeks into my plan with NBT I was diagnosed with Type 2 Diabetes.  I already had all the markers of metabolic syndrome (obesity, high blood pressure, excess abdominal fat, high triglycerides, low HDL cholesterol, high fasting blood sugar).  This latest diagnosis really got my attention.  I had suspected diabetes, but it was actually confirmed by someone in a white coat, and Metformin was prescribed.  I took that for 5 days and then quit, committing fully to the NBT recommendations instead.

The Process:

Overall I’ve been very happy with how things are going.  In the last 3 months I’ve had the following results:

Blood sugar:

  • Before: When I started my fasting blood sugar averaged 146, and post prandial (2 hours post-meals) averaged 149.
  • Now: Fasting blood sugar over the past week averages 103.  Post prandial blood sugar averages 95.

Weight loss – Down 16 pounds from 207 to 191.  My fancy scale tells me I’ve lost 4 pounds of water, 10 pounds of fat and 1 pound of muscle.  I have done some walking 2-3 times a week, but otherwise no real exercise during the past 3 months.

Energy/mood/libido – Vast improvements in all of these areas.

I’ve had some bumps along the way, most notably when I decided to add dairy back in to my diet for a couple of days (note: this was NOT the recommendation of NBT).  Also, most recently adding prebiotic fibers (to feed the probiotics), I got to remember what it’s like to feel depressed.  Needless to say I’ve again quit dairy and fibers.

The best part about this process has been learning that there are little-known SCIENTIFICALLY SOUND medical interventions that some doctors and practitioners are doing, based on testing.  None of this get-on-facebook-and-fix-yourself kind of stuff I was doing for the last 3 years – there are amazing tests that give you a ton of information about your state of health and there are amazing products to support your recovery.  Guessing is absolutely not necessary.

Going Forward

I’ve got a coaching call scheduled with Chris Kelly on Monday.  Depression has abated since I quit the fibers but fatigue and bloating are now present – these were gone and now they’re back.   Also, I haven’t lost any weight since I added the fibers in 10 days ago.  Not ok – I still have 30-40 pounds to go!  I’ll be doing a ubiome test to see what’s going on in my gut these days.  I’m considering another round of antimicrobials to undo whatever I did with the fibers.  Lots of variables.

Off Center

I can’t quite regain my footing since adding the supplemental fibers to my diet.  I’m crying off and on, far more than I have been at any point in the last 3 months – sometimes at work, which is really fucking embarrassing.  I just feel mildly depressed again.  Energy is ok but mood is low, enthusiasm is low, irritability is present (where it wasn’t 2 weeks ago).

I don’t know if this will just pass or not.

Depression and Labs

Long one today…

The probiotic part of my plan hasn’t been without it’s ups and downs.  Most recently there have been more downs.  I started taking Prescript Assist a couple weeks ago.  It gave me headaches, poor sleep, and sugar cravings.  So I stopped it, and all of that went away.  In the meantime I started taking some other probiotics I had lying around (which absolutely did NOT interfere with my new baseline of fabulous).  Unfortunately I ran out of those and they’re no longer being manufactured. I tried adding in the Prescript Assist again gradually this past week – first once a day, then twice a day.  Poor sleep again, and sugar cravings again.  No headaches though.

And then…I seem to be be having a bad reaction to my bionic fibers. My functional med practitioners recommended adding Inulin, Glucomannan, and Acacia fibers as prebiotics to nurture along the probiotics.  I have had a bad history with prebiotics, particularly inulin and potato starch, so I wanted to approach this slowly.  I started with about 1/6 of the recommended amount, and added a little more each day.  Yesterday – about 5 days into this process – I became very depressed.  I couldn’t stop crying at work and basically had to leave my office and go sit under a tree in the woods for a while.  That’s the first time I’ve felt depression in months.  I’m sure it’s due to the use of the fibers, maybe in combination with the Prescript Assist.  Dunno for sure who the real bad guy is.  Sugar cravings were crazy yesterday too.  I eat absolutely no sugar or starch on a day-to-day basis, and never miss it.  In fact lately I don’t care much about food one way or another except that it makes my hunger stop.  But yesterday I couldn’t stop thinking about sugar.  I grudgingly ate some M&Ms so I could get on with my day. (<– Seriously.  There was no joy in it. I ate M&Ms the way some people mow their lawn.  It was just something I had to do.)

I’m beginning to think I’m nothing more than a ball of electrical impulses controlled by bacteria.  Acutally, it’s becoming quite clear that that’s not far from the truth.

I wrote to Amelia for guidance and she recommends stopping the fiber and probiotics for now and restabilizing.  I’m going to take her advice, but I may trial a different probiotic after a couple of weeks.

Ok, next order of business: labs.  I had some lab work done to measure progress so far.  Right now I’m a week shy of 3 months on the supplement protocol recommended by my friends at Nourish Balance Thrive. In general I feel amazing (yesterday’s depression being a ridiculous and unusual aberration at this point).  Let’s see what the numbers say.

Keep in mind, this is the progression of events in my world:

  • In 2012 I was eating low carb/paleo including a couple months of cold thermogenesis, not much exercise.  Lots of emotional stress toward the end of the year (11/2012).
  • In October 2013 I started following Ray Peat’s principles and was well into it by 7/14.
  • In February 2015 I went back to paleo – no sugar, starch, or dairy and started NBT’s recommended supplement protocol.

Current labs are in red.

We’ll start with my basic metabolic panel (click to enlarge):


The good:

  • Blood sugar – much improved with current program.
  • AST/ALT – liver enzymes coming down a little.

The bad:

  • Uric acid – higher than before but not out of range.
  • BUN/Creatinine Ratio is high now – showing signs of kidney strain?  I have been eating much more meat since I stopped eating everything that tastes good.
  • Potassium is low. This could be because of the hydrochlorothiazide I’m taking for my blood pressure.  Amelia told me to supplement potassium and I stopped doing it when the bottle ran out.  Oops.
  • Carbon Dioxide – Pretty low.  Ray Peat would be displeased.

How about the lipid panel (with some other stuff mixed in):

lipids other

The good:

  • Triglycerides are down (still high, but down).  Amazing to me that they could be so high given the complete lack of carbohydrate in my diet.
  • HDL up a little from last time but still not fabulous.

The bad:

  • Cholesterol and LDL still high
  • C-Reactive Protein (HS) – still high.  I was really hoping that would have come down by now.
  • Estradiol low (don’t know if this is a bad thing, actually)

Thyroid Panel:


The good:

(…what’s that I hear?…)

The bad:

Let’s see, where should we start…

  • Reverse T3 is way up.  Stop the Thyroid Madness says my Rt3 ratio (the ratio of T3 to Reverse T3) is 12.5.  Ideal is over 20.  This suggests that T4 having trouble converting to T3 and instead is turning into RT3.  This happens under stress, from what I understand.  I’m not under emotional stress right now, which suggests I might be under physiological stress.  Ray Peat might be right about us needing carbs.
  • TSH is up a bit
  • T3 is down (But not free T3.  Don’t know what that means.)

And finally, CBC:


Nothing remarkable here, which I assume is good.  I don’t really know how to interpret the CBC part of the testing but things are all in range.

So, did I miss something?  Please feel free to share your interpretation of my labs in the comments.

So overall thyroid is struggling but liver and blood sugar are better.  In my current state of health, that’s the choice I’ve made up till now – I was warned that low carb might tank my thyroid, but I did it anyway because my diabetes was pissing me off.  So what’s the plan?  I probably need to start exercising so I can incorporate carbs into my world again.  So that’s next up.

Bring on the kettlebells.