Autoimmune diseases are increasing at alarming rates. Everyone has their theories as to why this might be happening and there are so many autoimmune diets and treatment protocols going around it becomes confusing to the layperson as to which path to take.
Thee are several areas of the body which need attention when you are trying to treat or prevent an autoimmune disease, but to date most of the treatment protocols that are being given out to patients are making some glaring mistakes and certain areas which need treatment are being totally overlooked.
Let me point out these gaps in the treatment of autoimmune disease so you can understand at a deeper level both issues: first, which areas of the body need attention and second, precautions which need to be taken as you treat these areas. Otherwise you could either feel a little better and reach a plateau where you can’t make any more progress or you could actually get worse as time goes by.
First, it’s important to know what exactly is the immune system, so you know which areas need attention.
The immune system is the gut microbiome, the liver and the bone marrow. All three need attention, but from what I can see only the gut microbiome is receiving attention and the liver is receiving incorrect attention, if any at all. And as far as I can tell, no one is focusing on the bone marrow, which is totally neglected in most of the treatment plans that are given out.
Let’s take a look at these three issues and then I’ll show you some pitfalls you want to avoid.
First, let’s start with the gut microbiome which consists of friendly bacteria overseeing some potentially bad guys, such as pathogenic bacteria, candida albicans yeast, fungus, viruses and parasites. All these organisms actually play a role in our health and they live in harmony with us, as long as the friendly bacteria, their surveillance team, remains intact.
But there are far too many pharmaceuticals, such as antibiotics, birth control pills, steroids, acid reflux medicines and others, which can destroy these friendly bacteria, allowing the potentially bad guys to damage our health as they overgrow as much as they want since they are now left unchecked. And stress also depletes the microbiome as much as the pharmaceuticals do.
These infections create responses from the immune system which create inflammation. In addition, the gut becomes leaky, allowing poisons such as the lipopolysaccharides from the gram negative bacteria which reside in the gut and normally exit into the bowel movement to now absorb into the bloodstream. Once these poisons seep into the bloodstream, the immune system cranks up a huge response, creating massive amounts of inflammation as a result. Now you have two huge sources of inflammation stemming from the gut: from infection and from toxins leaking through.
And since the gut represents 80% of our immune system, it begins to lose its intelligence and starts to attack the body as it spirals out of control, creating the perfect situation for an autoimmune disease to develop.
There are two ways to fix the gut, but neither one is effective if you don’t know how to do it correctly for reasons which I will describe here.
First, we could use probiotics, but here’s the pitfalls to look out for. Most of the active probiotic cultures on the market die as they are being processed..This ultimately led to many lawsuits as the probiotic companies only stated the active cultures which were alive in the beginning of the processing. It is now recommended to put exactly how many live cultures are present at the end of the processing so you know its exact potency.
Second, even if the cultures are alive, they have to make their way past 3 barriers: the stomach acids, the bile acids and the pancreatic enzymes, all of which can destroy the delicate probiotic cultures before they even make their way into the intestines.
Which means you have to find a company which knows how to protect the live cultures as they go past these barriers.
The better way to repopulate the gut is to make yogurt either with A2, non-homogenized whole cow’s milk from grass-fed cows or from goat’s milk if you are allergic to cow’s milk. The problems with the yogurts being sold in the supermarkets and health food stores is that their cultures are not strong enough since they don’t replenish the cultures enough. So when you make your own yogurt make sure you use your yogurt starter every two months or else your probiotic cultures won’t have enough of a therapeutic value.
And when making the yogurt avoid keeping it in the yogurt maker longer than 10 hours. The longer they are allowed to develop, the more acidic they become. The ancient Ayurvedic doctors said the yogurt should taste alkaline since these acids could actually kill the friendly bacteria contained within the yogurt. I personally like making yogurt using an Instant Pot which has a yogurt setting, since many of the yogurt makers keep the temperatures too hot.
We also recommend making buttermilk from the yogurt where you mix 1/4 cup yogurt, 3/4 cup water, 1 pinch of ground cumin and 3 cilantro leaves blended for one minute. Sip on this in between bites of food at lunchtime only. The ancient doctors were so wise to recommend sipping on buttermilk in between bites of food. It turns out that the food will protect the live cultures as they make their way past the barriers.
Yogurt should only be taken at lunchtime because our digestive fires are too weak to properly digest it in the morning and the evening.
This means that through the night your capability of digesting food, known as the digestive fires, are out while you are asleep. In the morning as the sun begins to rise your digestive fires start to ignite and by the middle of the day when the sun is the highest in the sky your digestive fires are also the strongest. Then as the sun goes down your digestive fires go down, which means that you should never take yogurt in the morning or the evening since it is cold dairy, which could clog the physical channels of the body since it is putting out the digestive fires which are trying to ignite. This is also why we don’t recommend drinking cold smoothies first thing in the morning.
At the same time you fix the friendly bacteria in the gut you have to build up the mucus layer in the gut. This mucus layer is the substrate in which the friendly bacteria grow, and it too gets depleted from the pharmaceuticals previously mentioned.
We recommend using slippery elm, marshmallow root and deglycchyrized licorice, all of which are slimy and are great for building up the mucus layer. Eating ghee in the diet, raw honey and lots of fiber in fruits, vegetables, grains and beans also help to regrow the friendly bacteria by giving food for the friendly bacteria to eat. Watch my video on butyrate so you can learn which foods to eat to promote the growth of this short chain fatty acid which has the capability of also building up the mucus layer.
Next in our treatment of autoimmune diseases, we have to look at the liver, since this also plays a huge role in our immune system’s responses. Most people know we need to clean the liver, but this is where everyone makes huge mistakes which can backfire on you creating more of an autoimmune response.
The problem is that the liver is the main filter in the body: the blood comes in dirty and leaves clean. But in this modern era it is overwhelmed by all the 80,000 chemicals we have surrounded ourselves with in the food we eat, the pharmaceuticals we take and the environmental pollutants which are everywhere.
So yes, we are correct to say that the liver needs to be cleaned like any other filter, but the trick here and this is very important: when the liver is holding onto a lot of toxins it becomes very hot and reactive, also allowing inflammation to spread from the liver into the whole body since the liver makes the blood from the food we eat.
This means that when we clean the liver we need to keep it cool at the same time. Which also means that most of the herbs which clean the liver, such as milk thistle, dandelion, burdock root and even our Ayurvedic herbs such as guduchi, kutki and several others will heat up the liver as they clean it. In fact, milk thistle is the worst of all of these and this is the most common herb I see many people take when they have an autoimmune disease.
In my practice we use an herb called bhumi amalaki, or bhumi amla for short, since it is the only herb that can clean the liver and keep it cool at the same time. The ancient doctors of India said bhumi amla would take care of the liver like a mother, nurturing it as it cleans it, unlike milk thistle which tortures the liver as it squeezes the toxins out, heating it up along the way, thrusting you deeper into your autoimmune disease.
We also use herbs to regenerate liver cells, especially if you grew up eating white refined processed sugar or refined vegetable and seed oils which turn into poison when you cook with them. And since everything you swallow is being processed by the liver, because it is also the seat of digestion, these oils and sugars end up damaging the liver, creating scarring in many of the liver cells and fatty liver in many people who don’t even drink alcohol, which is also famous for causing a fatty liver.
And finally, the third part of the immune system is the bone marrow. This is where the immune system cells are born, so we want to make sure no toxins enter here. In Ayurveda the bone marrow is considered one of the deep tissues, hidden inside the bone, preventing toxins from entering. However, many pharmaceuticals make a beeline for the bone marrow and every day when you step outside and breathe in the air pollution, these chemicals also go into the bone marrow, as do pesticides and many other chemicals.
So you need to clean your bone marrow with remedies which also keep the liver cool. We give our patients teas made with coriander seeds, moringa oleifera and my favorite herb for cleaning the bone marrow, guduchi satwa, also known as Stem of Guduchi. We also instruct them in the use of moringa sticks, which are from the moringa tree and are also known as drumsticks.
I have made a video on coriander seeds and one on Guduchi Satwa, so you can have a deeper understanding of these two potential players in treating autoimmune diseases. I have also made a video on moringa so you can see what the moringa leaves and sticks look like.
There are many other things to consider, such as the diet, the bedtime and daily routine and then the seasonal cleansing techniques which you should be doing every spring and fall.
So you can see very quickly by the information I have included here how and why most people aren’t overcoming their autoimmune diseases, because there isn’t enough detailed information out there.
This is because most of the Western world does not have an ancient tradition of healing and are trying to heal people with nutraceuticals which are the toxic version of the real thing. Nutraceuticals are the synthetic vitamins which are being recommended by many practitioners since most modern cultures haven’t ever figured out what herbs they have available to them and the correct use of those herbs.
I made this video because the vast majority of the patients I see do have autoimmune diseases and are getting worse due to these insufficient and incorrect treatment protocols which do not pay correct attention to the liver and no attention paid to the bone marrow.
Instead people are being given lots of remedies to take without any knowledge of the fact that the patient will feel worse on them as their beleaguered liver has to now contend with either herbs that are heating it up even more or nutraceuticals, which are highly toxic to the liver. They just sound good because they were originally discovered in food. The mistake we made was that we thought we could isolate the active ingredient out of the food and make it in a lab. As if the active ingredient is the only thing in the food that has any value.
I hope this information gives you some deeper insight into the correct way to treat your autoimmune disease. I discuss all this and more in my new book coming out in 2026 by Inner Traditions publishing company. Stay tuned for more details on the book.