Organic and under-nourished: gut rehab, genetic influences, and supplements

What if your diet is clean, yet you are not quite as healthy as you know you can be? Why are you feeling exhausted when you get 9 hours of sleep? When I was diagnosed with an autoimmune condition, I wanted to know what I could do in my daily life to get back to health, but there were few good leads.

It's only been in the last few years that the scientific community is taking leaky gut seriously and recognizing the contribution of gut dysfunction  to a growing prevalence of autoimmune disease.

As someone who eats organic, grass-fed, reads labels, and generally eats very little processed foods, basic information about good nutrition is not that useful to me. Yes, I know the deficiencies in the Standard American Diet. Yes, I already avoid having my meals at fast food restaurants.

Once you get past the basics, there is so much contradictory advice on healthy ways to eat and I am not fond of extreme dietary approaches. For those of you past the basics, I am going to share what I learned about gut health, the immune system, and nutrition for your benefit.  If you have gut issues of any kind (sharp pains, bloating, cramps, food that feels like it sits too long in your stomach after a meal, constipation, diarrhea), or if you have any chronic condition and you want to understand how nutrition can contribute to your healing, here are my cliff notes to help you get over the first big waves of information. Hopefully it may point you down a path that is specifically appropriate for your issue.

Methylation, endocrine negative and positive feedback systems, galactans, methionine cycle, histamine intolerance, innate and adaptive immune responses, sympathomedullary pathway, cytokines, homocysteine. These are just a few of the terms you might come across when trying to understand immunity, hormone function, and digestion. They are also issues you might encounter if you are looking at gut health. I've summarized four points to help sort through the mass of info out there and get you started on healing through nutrition:

1. Genetic profile matters

They say that personalized diets are not far off. But in the meantime, we clearly know that there is no one perfect diet across the board. In fact, a "healthy" diet may contain all the inflammatory foods that you should avoid, or it may eliminate exactly what you need.

You can expect that if you have an autoimmune condition, you probably have some level of defect in methylation. I took the 23andme test to determine to what degree I had genetic mutations (technically a polymorphism). If you decide to get your DNA profile, these results must be interpreted through Because of this ploymorphism, the B-complex supplement I was taking was toxic for me. I cannot convert the hydrochloride form of B6 in the supplement. If you have a specific genetic profile that diminishes methylation, you also cannot convert folic acid, a synthetic form of B9. Dr. Kresser is a reasonable voice when it comes to this body of info.

The most significant thing to know about methylation is its role in turning on and off genetic encoding. If you are genetically disposed to deficiencies in certain essential biochemical processes, you need to be more diligent about addressing your specific needs. 

Genetic tests may also reinforce and justify use of supplements. I am very reluctant to take supplements without good reason. In my case, vitamin D and a methylated form of B12 is indicated based on my genetic profile. It's still not verified by the scientific community as this is emerging science, but functional medical doctors use it clinically with success. It was part of my path to remission. If nothing else, it justified specific supplement intake.

2. Nourishment vs. detox

Healing the gut presumes some type of chronic dysfunction. It is a slowly depleting process. A depleted system needs nourishment, not cleansing. I live in Los Angeles, and the prevalence of cleanses and detox approaches is rampant and often unbalanced. Detox and cleansing is appropriate if you have been binging or otherwise had an acute overload. It is a process of stripping out. If, however, if you already have a pretty clean diet, an aggressive detox can deplete a system that doesn't require it.

Nourishment typically means more fats, protein, and minerals. Grass-fed sources of saturated fats, animal protein, and bone broth are good ways to restore a distressed digestive system. This nourishment should always be balanced out with extra vegetables. Across all forms of eating styles, increasing vegetable intake, particularly green vegetables, is non-controversial. Bieler's Broth is a particularly good way to meet extra vegetable needs for a depleted system.

3. Change food first to heal the gut

Nutritional consultant Margaret Wright was the first to cue me into specific genetic limitations that may contribute to biochemical dysfunction, basing that on my lab results. This started me down the path of eliminating foods that I previously would not eliminate. Functional medicine Dr. Amy Meyers, through her book, videos, and writing, helped me realize that eliminating gluten was not enough when you have an autoimmune condition.

I strongly encourage you to make the effort to change how you nourish yourself to support any medical approach you are taking. If you are constantly under-nourished, you may respond poorly to any medication, radiation, or surgery.

Whole30 is a good place to learn about an elimination diet.  The Perfect Diet is another source worth examining.  In most elimination diets you are removing grains, dairy, legumes. Another layer of elimination may include nuts/seeds, nightshades, eggs, fermented foods. That second layer of elimination was necessary for me in the first phase, but I have eventually brought that layer back in.

4. Supplements are not harmless

By starting with food first, I was able to gradually add specific supplements and watch their effect. How effective are supplements if you are burdening your system by the foods you eat?

As I said earlier, taking a vitamin B complex merely because I had Graves was not good for me, but I was running out of non-medical options. Do not supplement based on the diagnosis. Understand your specific genetics and state of health, as well as the nature of synthetic supplements. If you are quite unwell, supplement under the guidance of a functional medical doctor. Graves can be a serious condition so I am under the care of a thyroid specialist from the medical side. I got into remission through food only, but I can refer to her should my condition need medical assistance.

I believe you need to be motivated to avoid medications. I introduce supplements slowly to discover what recommended supplements work for me. Many multi-vitamins may contain forms you cannot convert, contain elements that you need less of, not more, or otherwise be inappropriate for your state of health. I use my subjective experience of energy level and endurance, plus labs to determine what is working for me. You can order your own labs through Direct Labs or Health Check USA. Bloodwork can be expensive and confusing, and you should be organized to track them, so it is best to have an initial test under the guidance of a medical professional as a starting point.

I hope these points have been helpful to move you on a path towards greater health.