Hi friends. I recently taught a class on using herbs in acute and chronic respiratory infections. Here is the class description: 

Prepare for winter by enhancing your understanding of how respiratory infections develop and how herbal, nutritional, and lifestyle interventions can make a big difference regarding prevention and recovery. In this class we will discuss how to use herbs to address a wide variety of respiratory complaints including colds and flus, acute and chronic lung infections (bacterial, fungal, and viral), bronchitis, as well as chronic sinus irritation and infection. Our focus will be on moderate to severe respiratory illnesses. Students will gain deeper knowledge of how to use natural means to combat infections in order to minimize the need for use of antibiotics, steroids, and other pharmaceuticals.

Below is the lecture, which is split in two parts. I've also added a slide show of my power point slides. Enjoy! Let me know if you have any questions or would like to share your own experiences. 

I have some wonderful things to report after several weeks of self-experimentation. I've been inhaling essential oils since late February, and after seven weeks I feel like I have enough of  consistent results to report my findings (I am a scientist, after all). 

First of all, before I started inhaling essential oils I had just gotten off of oral antibiotics (minocycline and bactrim) and was planning on going into the hospital for some IV vancomycin to treat my MRSA infection. Fate brought me a snow storm that prevented me from getting to the hospital, and instead I decided to test out the eucalyptus essential oil I had bought the day before. I am so glad things worked out the way they did, or I would never had made these radical discoveries!

Why Use Essential Oils?
It's been on my mind for many months now that I should begin inhaling essential oils. In herbalism school we talk a lot about plant constituents, and that those herbs that are the most antimicrobial (antibacterial, antifungal, antiviral, etc.) contain a high amount of volatile oils. 

Coughing up blood ain't no fun, and sometimes it can be kinda scary. I began to see blood in my sputum once in a while beginning in high school. Now it's a bit more frequent and in larger quantities, but I don't let it get me too worried anymore because I know how it works and what to do in an emergency. I thought I would talk about hemoptysis a little bit here, as it is something you might run into, and it can be scary for someone who is new to it. Some of these things can be worrying to think about, but ultimately the point of this post is to inform you of the possibilities so that you are prepared to do what needs to be done in these situations. By asking questions and learning as much as I could about this topic, I've faced my fears and eliminated the anxiety I used to have over coughing up blood. Now I know what to do and am unafraid. I hope this info can help you, too. 

 What it is
Hemoptysis (coughing up blood) is a result of bronchiectasis, which is the scarification and weakening of the walls of the bronchioles in the lungs. When the little airways in our lungs become scarred and lose their elasticity, any kind of trauma (i.e. coughing) or inflammation can cause them to tear or collapse. When this happens, blood from an adjacent bronchial artery can flood into the airway and into the lungs, causing us to cough up that blood. Most of the time a very tiny bit of blood gets into the airway before the body quickly repairs the tear with a clot or by clamping down on itself to staunch the bleeding. This is when we see streaking in our sputum or when we get a small (a teaspoon) and quick bout of pure red blood. When larger bronchioles tear it becomes a little harder to create a clot quickly, so a larger amount of blood can get into the lungs. This is when you get several tablespoons to a cup of blood out. The body is very good at finding ways to stop the bleeding, and even in a situation where a cup of blood is coughed up (I've had this happen, definitely scary) the body will usually find a way to clot the tear or staunch the blood within a few minutes. For more info on hemoptysis, visit my page CF 201. 

The Cause
A teaspoon or a couple of tablespoons of blood is nothing to get scared about, however it is a signal that something down there needs some attention. It is a sign that you are battling an infection or have some acute inflammation in the lungs that is exacerbating your bronchiectasis. For me, this is usually a sign that I need to focus my attention on reducing inflammation (either through antibiotics or paying closer attention to my diet and supplements). I can also sometimes get it in times of acute stress, excitement, or exposure to an environmental pollutant, like hanging out around a campfire. In addition, if I have an acute infection and I do some kind of strenuous aerobic activity that causes me to huff and puff and cough heavily, that can also trigger hemoptysis. When I'm sick, I'm obviously going to continue exercising and doing aerobic activity, however if I see streaks in my sputum that day, I'm gonna tone it down a little to allow the body to heal that tear so it won't get any worse. 

I usually get hemoptysis right when I lay down in my bed to sleep. I think that the sudden change in airway pressure from standing to laying down can cause the little bronchioles to collapse or tear more easily. When I know that I am at risk for some hemoptysis that day, I ease into the horizontal position by first reading in bed for a few minutes in a reclined position propped up on a pillow. This usually works as long as I first lay with the non-bleeding side down (if you can tell which side it's coming from). 

Everyone's hemoptysis is going to be a little different, and so the triggers will be a little different. I've learned to notice the subtle changes, feelings, and sounds in my chest that may alert me to the risk of hemoptysis. The key is to pay close attention to your actions and what could be causing the hemoptysis so you can reduce your risk. A lot of it is out of our conscious control, however we can always do something, big or small, to help or hurt the situation. 

What to do
If there are infrequent streaks of blood in the sputum, it's not that big a deal so there isn't really much you need to do other than keep an eye on it and think about how you could take further action to reduce your inflammation. 

If you cough up a small amount of pure blood, somewhere between a teaspoon and several tablespoons, I've been advised to stop using pulmozyme for 24 hours. Pulmozyme is designed to break up mucus, but it can also break up a fresh blood clot. I continue to do the rest of my treatments normally. Also, try not to do any overly-strenuous aerobic activity that's gonna make you cough hard. It's very important to continue exercising, but maybe choose something more mild, like walking, biking, or yoga. Rarely if ever does yoga cause me hemoptysis, even though there are inversions and a lot of laying down and getting up. But again, you're gonna have to see how your unique body responds. After coughing up pure blood, reflect back to see if there were any particular triggers. Did you eat something inflammatory? Where you exposed to any pollution? Did you get really stressed out today? Were you exercising too hard? Do you feel an infection coming on? And make sure to eat as many anti-inflammatory foods and supplements as you can, including vegetables high in antioxidants, healthy fats, fish oil, and anti-inflammatory herbs. 

If you cough up a lot of blood, like half a cup or more, you need to call your doc. They can advise you on what to do. Sometimes people can cough up a cup of blood once in their life and never do that again. Sometimes keeping on top of your health with good diet, exercise, and diligent adherence to your treatments can prevent big episodes and resolve the issue. In these situations, no further action needs to be taken. I've coughed up more than a 1/2 cup of blood twice, and each time it was a sign that I needed an admission. The second time I got more serious about considering a pulmonary embolism. Since I was doing pretty much everything I could with my diet, exercise, and treatments and still the hemoptysis was happening, it was time for me to consider a more serious intervention.  

If you cough up blood and can't stop, call 911 and get to the hospital! I have been told that although hemoptysis is very common is CF, this kind of emergency where someone can't stop bleeding is very rare. Almost always the body is able to find a way to stop the bleeding. But it is good to at least be mentally prepared for the worst and understand how to manage it if it happens. If the blood doesn't stop, the risk is that you might drown. Yeah, that's a frickin' scary-ass idea, huh? It doesn't happen right away though, maybe within an hour or so. By then an EMT will have intubated you and you'll be fine, on your way to the hospital for an emergency embolism. I've also been told that laying on the side that is bleeding is a good idea so that the other lung will be prevented from getting any blood in it. Again, I've been told by multiple doctors that this pretty much never happens because people usually get an embolism way before things get this bad. So don't lose sleep over it. It is a scary thing, but fear does us no favors. I've prepared myself for this very rare possibility by educating myself as to what could happen and how I should act if it does. Knowledge is power, and so it helps to allay my fears when I know more about the situation. That's why I'm writing this post, to help others be unafraid in the event that the worst happens. 

Bronchial Artery Embolism
If you've had several big episodes of hemoptysis, or your hemoptysis is getting worse and more frequent, it may be time to ask your docs about a bronchial artery embolism (sometimes called a pulmonary embolism). It is a procedure where an interventional radiologist attempts to pinpoint the spots that your lungs are bleeding and to embolize them. The word embolism means to create a blockage in a blood vessel so that blood can no longer flow through it. If you are no longer actively bleeding, before you get the embolism your pulmonologist will most likely do a bronchoscopy to try to find any evidence of the spot that is bleeding, ideally by finding the clot or evidence of leftover blood. If they can find the spot, that's really great because it will help the radiologist find that spot from the arterial side and embolize it more quickly. If they cannot find the spot, it is still possible for the radiologist to do the embolism because they can do a contrast x-ray (where they inject you with radioactive dye and map your arteries under an x-ray machine) of the bronchial arteries, mapping your branches to see where  are possible spots of bleeding. This is what happened to me - they couldn't find the spot with a bronchoscopy, but they found plenty of spots with a contrast x-ray. So we did the procedure anyway and I'm glad we did. 

Small bronchial arteries run alongside our smallest airways (bronchioles), which provide oxygenated blood and nutrients to our lungs. When an airway collapses it allows the adjacent bronchial artery to bleed into the lung. When an airway is having trouble fully healing and is breaking open over and over again, one solution is to embolize the adjacent artery so that it can no longer bleed into the lungs. This is done by shooting tiny plastic pebbles into the artery to block it up. If you know your anatomy, you may be thinking: Wait, won't that kill the lung tissue because it will be denied access to blood? The answer is yes, to some extent. But embolizing usually does not cause a significant damage to the lung tissue because our lungs create redundant connections to a fresh blood supply. But an embolism will cause at least a little bit of tissue death. This is why it's a last resort procedure that you don't want to do unless you really have no other choice. There's also no guarantee that the radiologist will embolize the "right" spot that is causing the bleeding - it's really hard to see what you're doing down there. Some people have to do it a few times to get relief.

If you've got a significant amount of bronchiectasis like me, you've probably got plenty of spots down there that have bled in the past or have the potential to bleed in the future. So even if a bronchoscopy can't find "the spot", a radiologist will most likely be able to find several places that are at high risk for bleeding and will embolize them as a preventative measure. This was the case for me. My bleeding is not completely gone, but it's significantly reduced and now I only bleed when I'm very inflamed, maybe once a month (as opposed to every week or so before the embolism). 

I've had one embolism, and sometimes people have them done several times. But what does it feel like? Well, I can tell you the brochoscopy was the worst part of it for me. The actual embolism is super easy because you're gonna be sedated, and with versed (the nice stuff) not general anesthesia. The procedure itself doesn't hurt, but there are three possible issues that are not fun to deal with: 1) they have to access the bronchial artery through an incision near the groin. If you're a prude like me, this is not very appealing (but I did it anyway and it was fine). 2) After the procedure you have to lay down straight and not move for 4 hours because the arterial incision has to heal - no hemorrhages please! If you're unlucky, you'll get to experience what it's like to have to use a bedpan. Trust me, it will provide great material for jokes later on. 3) A day or so after the procedure you may feel weird pains in your chest that feel like intense muscle aches or cramps in the ribs. I'm pretty sure it's not the muscles that hurt me but the pain that I felt from the lung tissue death and the resulting inflammation that is needed for the body to clean it up. This pain may last a couple of days, and may even come with a fever. Although it's kinda painful, it does go away and it is just a sign that your body is cleaning things up and healing. 

Conclusion
So that's a bit about hemoptysis and what to do about it. Ideally with a healthy diet and lifestyle we can reduce our bronchiectasis and prevent hemoptysis from happening. But in case it does happen, it's good to be educated on what choices you have. This is a pretty scary topic for most people, and some people would rather stick their heads in the sand and not think about it. But it is my opinion that the more informed we are, the more prepared we can be in these situations and the less scary they become. I've had a lot of fear about coughing up blood in the past, but I faced that fear head on and got over it. It doesn't scare me anymore, and I am much less anxious about it when it does happen. I feel a little bit more in control and prepared for the possibilities. Again, being informed is being empowered. I hope this helps. 

Update: May 2018
A few years ago a new application for an old drug came across my radar: tranexamic acid. It is a drug that has been used in Japan since the 1960's to treat post-partum hemorrhaging in people who just gave birth. When I read that article I immediately thought: woah, we CFers could use something like that! So I asked around and it turns out that a couple of clinics had been experimenting with it for use in hemoptysis with good results. I asked my CF docs about it, and they had never even heard of it. There is precedent for its use in CF hemoptysis, and several CFers that I've spoken with have found it to be very helpful in acute bleeds. So if you think you might benefit from it, please ask your doc about it. I want more people in the CF community to know about this potentially life-saving therapy. 

For those of you who have already read CF201 and don't want to dig through the whole page once again to find my new material, here are (most of) the sections that I have added/updated:


Bronchiectasis and Inflammation
CF is described as a classic example of chronic inflammatory disease. Bronchiectasis, the main constituent of CF lung disease, is the result of out-of-control inflammation. It is described as the over-dilation of our airways to the point where they lose their elasticity and scarify. This causes the airways to become fragile and increases the risk of them collapsing or breaking, which can lead to hemoptysis (bleeding of the bronchial arteries into the airways leading to coughing up of blood). Our airways over-dilate in part because they are filled with mucus, and in order to move any air through a clogged up airway, they must widen themselves. But bronchiectasis is also caused by neutrophilic inflammation and the airway scarification and restructuring that results.

The inflammatory processes that cause bronchiectasis are complicated and not fully understood, but much of the problem has to do with over-recruitment of neutrophils into the airways. Neutrophils are white blood cells that kill pathogens and help clean up infection. Under normal circumstances, these guys are wonderful and target infection quickly, clean it up, then move on. But in situations of chronic infection, neutrophils (NTs) never really move on. In CF the situation is even more complex. It turns out that CF lungs have higher than normal levels of NT elastase (an enzyme that NTs use to kill pathogens and break down tissue) even without pathogenic colonization [23,24]. We don't know why this is for sure, but I postulate that one possibility could be autoimmunity. In fact, cases of non-CF bronchiectasis in older Americans are increasing at a rate of about 8.7% per year, and it is often diagnosed in patients with autoimmune diseases, especially rheumatoid arthritis [24]. Regardless, neutrophils and the inflammatory mediators that they secrete (e.g. NT elastase, IL-8) cause further neutrophil recruitment, tissue damage, and airway remodeling (i.e. bronchiectasis) [23]. It has been found that the greater the level of NT elastase in CF sputum, the lower a person's FEV1 will be [25]. Not only does NT elastase break down the elastin, collagen, and protoeoglycans in the tissue of our airways, but it also makes our mucus thicker and harder to expel. This is a problem because thick mucus provides an even better home for pathogens to breed, plus it makes it harder for the NTs to move around in the airways, so they get stuck, die, and cause mucus pooling, which causes the airways to widen even more to get around the mucus pooling, causing further bronchiectasis. Pulmozyme (DNAase) works by breaking apart neutrophil elastase in the airways, making the mucus thinner and easier to cough out. 

Another problem with neutrophilic inflammation in CF is that although the NTs are called in to kill pathogens, they don't actually do a very good job because they are lacking in the antioxidant glutathione - the number one most important tool that NTs use to kill pathogens. It is thought that CF cells have a hard time secreting glutathione into intercellular space because of the faulty CFTR channel, so NTs have less access to this important antioxidant. Several studies have looked into reducing systemic inflammation by boosting NT glutathione levels with NAC supplementation. N-acetylcystine (NAC) is a molecule necessary for the synthesis of glutathione in the body, otherwise called a glutathione precursor. Direct supplementation with glutathione is largely ineffective because it is easily oxidized by environmental factors. For years NAC has been used to boost glutathione in the lungs of CF patients by inhaling it in a prescription called "Mucomyst". This was effective, but went out of fashion as pulmozyme came along, plus I've heard that mucomyst wasn't so popular because it had a rotten egg smell when aerosolized. Now there is more research suggesting that oral supplementation with NAC may also be effective in boosting NT glutathione in the body as a whole and in the lungs in particular, making our immune system more effective at clearing infection. In a preliminary study, oral NAC supplementationsignificantly boosted NT glutathione and blood glutathione in the whole body, significantly reduced the number of NTs in the airways, significantly reduced IL-8 (an inflammatory marker) in the airways, and significantly reduced NT elastase in the sputum [25]. This is a big deal! This means that instead of dealing with systemic inflammation through palliative treatments like steroids, high-dose ibuprofen, and azithromycin, NAC supplementation targets the root cause of the problem with a completely harmless treatment that has virtually no side-effects and no known level of toxicity! A larger clinical study has just been concluded on the effect of NAC on CF lungs, and I look forward to exploring the results when they're published. The standard dose for oral NAC is 600 mg three times a day, and you can ask your doctor for a prescription for it. It is used in modern medicine to treat tylenol poisoning and interstitial lung disease, so your doc should be able to get your insurance company to cover it no problem. If not, you can also get it over the counter. There's a lot of interest in the CF community in a new over the counter form of it called PharmaNAC. 

Given all this, I have decided to focus on improving my lung symptoms by targeting inflammation as its main cause. I have struggled with bouts of significant hemoptysis in the last several years, and had my first pulmonary embolism in May. I have noticed that I get hemoptysis when I am particularly inflamed, caused either by a bad lung infection, inflammatory foods, and/or environmental irritants (e.g. campfire smoke or heavy pollen). Thus, in addition to adhering to the GAPS diet, I got my doc to give me a prescription for NAC, and we'll see if this improves things.  In addition, to treat systemic inflammation one must consider the role of gut inflammation, the cause of most inflammatory disease. Targeting the root cause of my systemic inflammation by focusing on the gut through improving my diet and cultivating a more balanced intestinal bacteria community has yielded very positive results so far, and I'm only in the very beginning of this treatment regime, so more progress is sure to come. 

Your Gut is Your Immune System
One way that your gut acts as part of your immune system is that the latter part of your small intestine, called the ileum, is lined with tissue called lymph nodes which kill and remove bacteria, viruses, fungi, and dead cells from the lymph (the fluid that circulates through the lymphatic system, exists in the spaces between organs, and interacts with the blood). In this way your ileum is a direct part of the immune system, and its ability to remove and kill pathogens in the interstitial space and the blood is critical to our health. When an infection is detected, the lymph nodes create lymphocytes which kill the pathogens, causing pain and inflammation in the lymph nodes. This means that if the lymph nodes in the gut are chronically exposed to toxins and pathogens, or if they have trapped pathogens within the nodes but can't clear them out, the ileum can become inflamed and painful causing serious digestive upset, reduced absorption capacity, and compromised immunity [28]. 

In addition, your body is an ecosystem that harbors over 400 species of bacteria just in the intestines themselves. But the whole body is populated by bacteria; the skin, eyes, nose, mouth, ears, genitals, lungs, etc. In fact, you have more bacterial cells in and on your body than you do human cells! In reality we are more bacteria than human. We are walking, talking ecosystems, and our bacteria keep us happy and healthy... if we keep them happy and healthy. Beneficial bacteria in the gut play a critical role in our immune system, keep pathogenic bacteria in check, help us break down and digest foods, and synthesize a number of nutrients that we cannot create ourselves including vitamin K2, folic acid, vitamins B1, B2, B3, B6, B12, and various other amino acids [28]. But in with our modern toxic lifestyles, it is becoming harder and harder to keep our beneficial bacteria healthy and our internal ecosystem balanced. Toxic foods, environmental pollutants, pesticides, antibiotics, pharmaceutical drugs, chronic stress, lack of exercise and time outdoors in the dirt, and many other factors have very negative effects on our bacterial populations, especially in the G.I. tract. For CFers, we have an added stressor to our inner-ecosystem, and that is our genetic defect of the CFTR channel. This makes it easier for certain pathogenic bacteria, viruses, and fungi to take hold and create an ecological imbalance. 

This is particularly true in the CF digestive system. Recent research has found that the bacteria that inhabit the gut early in life determines, in part, the bacteria that inhabit the lungs later in life. (As a side note, breast-feeding ensures an infant develops a healthy and diverse intestinal flora, so breastfeed your babe as long as possible!). The healthier the intestinal ecosystem is, the more resilient the lungs are to pathogenic bacterial infection. Thus, the guts and lungs are directly connected via their bacterial populations: "these findings are consistent with previous reports, with identification of bacteria in the respiratory tract in CF that are typically associated with the intestinal cavity and are theorized to contribute to the continuum of interactions between the host and microbial community in CF that relates to both the lung and gut microbiota" [26]. Although the biota of the guts and lungs are different, many species are shared between them, and this is especially true of pathogenic bacteria, like staph. Furthermore, it has been found that respiratory bacterial populations are not particularly diverse in healthy lungs, however the less diverse the CF lung is, the more severe the respiratory disease and the lower the lung function. And the less diverse the intestinal flora, the less diverse the lung flora will be as a result. In other words, the more species you have in your lungs and guts, the better your lung functions will be. This is very similar to measuring the health of an ecosystem (like a rainforest) by its biodiversity, i.e. the number of species that inhabit it. A decline in CF lung microbiome diversity is associated with antibiotic use, therefore antibiotic use is at least partially responsible for declining lung function: "[research has] identified that diversity decreased over time in parallel with progressive disease and remained stable in patients with milder lung disease; however, they identified antibiotic use rather than lung function as the most significant driver of decreased microbial diversity in sputum samples. Additionally, based on sputum samples, Stressmann et al. corroborated similar findings for 14 patients with CF that antibiotic use was most associated with decreased microbial diversity and that overall decreased diversity was correlated to more-severe lung disease, as well as abundance of pseudomonas aeruginosa" [26]. Thus, it is very important for us to use antibiotics sparingly and only when necessary, as they are particularly detrimental to the intestinal bacteria that keep us healthy and protect our lungs from further infection and domination by only a handful of pathogenic species. Plus, emerging research is showing that even one short-term round of antibiotics can permanently impact the intestinal ecosystem and reduce its biodiversity. What does that mean for CFers who have been on regular courses of high-dose antibiotics their whole lives? An intensely disturbed intestinal ecosystem and a high risk for all of the problems that come along with it (especially leaky gut syndrome). Inhaled antibiotics do not impact intestinal flora, and certain IV antibiotics like vancomycin also have minimal impact. But all oral antibiotics impact gut flora, and most IV antibiotics do as well (tobramycin, meropenum, ceftazadime, linezolid, etc.). Unfortunately, most CF docs don't know about this problem so they go on prescribing us antibiotics in complete ignorance of what they are doing to our guts and our immune system. They are pulmonologists by training, and allopathic medicine generally sees organ systems as separate and independent from one another. The latest research is blowing this last belief apart. So don't be discouraged if your doc doesn't know any of this. They were not trained in it, so it is up to us to educate them. 

Even more exciting is the research being done on treatment of the lungs through supplementation with oral probiotics. One study found that oral supplementation with only a single strain of Lactobacillus (GG) significantly increased CF childrens' FEV1, increased body weight, reduced the number and duration of hospitalizations, reduced the number of pulmonary exacerbations, and reduced the number of inflammatory markers (IgG). LGG and other Lactobacillus strains have a direct effect against Pseudomonas and have a systemic anti-inflammatory effect [27]. In conclusion, taking oral probiotics is extremely important for CFers, not only to restore intestinal microbial diversity, but to fight systemic inflammation and lung infections as well. But in order to restore ecological diversity in the intestines and the lungs, we should choose probiotics with as many strains of beneficial bacteria as possible. I discuss the use of probiotics more in my Supplements and Herbs section. 

Gut Dysbiosis and Carbohydrate Malabsorption 
The fundamental problem is that due to a number of factors including inheritance of your parents' intestinal bacteria (through the birth canal, breast feeding, and daily interaction), antibiotic or other pharmaceutical use, stress, poor diet, and pollution you have an intestinal ecosystem whose bacterial, viral, and fungal populations are imbalanced. The populations of beneficial bacteria that protect the health of your digestive system are reduced, and the populations of pathogenic bacteria and fungi (including Candida albicans) are flourishing. These pathogenic bacteria displace the beneficial bacteria that are so vital to digestion and absorption of food and maintaining a proper barrier between your gut and your blood. As the lining of the gut wall degrades, so do the cells that absorb nutrients from your food and that provide housing for the many digestive enzymes that break down your food, including lactase (the enzyme that breaks down lactose, milk sugar) and sucrase (the enzyme that breaks down sucrose, table sugar). Undigested carbohydrates like lactose, sucrose, and many complex starches are now being brought to the colon undigested where they feed the pathogenic bacteria and encourage their proliferation. As the population of pathogenic bacteria gets more and more out of control, the chemicals that they produce and the inflammation that they trigger begins to create openings between the cells of the intestinal wall, allowing undigested food particles (proteins in particular), bacteria, viruses, fungi, and bacterial toxins to move directly into the blood stream [28]. A vicious cycle has begun. 

From there a host of diseases can arise, depending on what types of toxins, pathogens, and proteins get passed into the blood stream and begin to circulate throughout the body. Bacterial toxins in the blood can make it to the brain where they can cause severe neurological diseases such as autism, schizophrenia, and bipolar disorder. Bacteria, viruses, and fungi circulating through the blood trigger a systemic immune reaction, leading to chronic infection and inflammation. Undigested proteins (the most notorious being gluten and casein) mimic the structures of certain proteins in your tissues, and as your immune system works to eradicate the foreign protein from your system, it begins attacking your own tissue that looks a lot like that foreign protein. This is known as autoimmune disease, and there are many modern diseases that are autoimmune (and thus digestive) in origin, including type 1 diabetes, rheumatoid arthritis, and multiple sclerosis. As you can see, so many of the chronic diseases that are so prevalent in modern society and that were virtually non-existant in traditional cultures are the result of eating a toxic diet that we are not evolved for and the gut dysbiosis that comes as a consequence [28,29]. 

Evolutionarily, a carbohydrate-heavy diet is a newfangled cultural artifact introduced less than 10,000 years ago. Depending on your ethnic background, your ancestors may not have been eating grains for that long, in some cases only a few hundred years or less. That is certainly not a long enough time for our digestive systems to evolve enough to subsist on them. Starches in the form of root vegetables have been eaten since the Paleolithic period, but only in small quantities and as a supplement to a fat-, protein-, and green-vegetable-heavy diet. Our modern diets of the Western world are extremely heavy in carbohydrates, specifically sugars and starches, which are very difficult for our Paleolithic digestive systems to digest. If continued long enough, adherence to this carb-heavy diet (especially the Standard American Diet, a.k.a. SAD) will begin to feed pathogenic bacteria and fungi in the intestines that thrive on simple sugars and starches. Gut dysbiosis results, and when those imbalanced bacteria are passed between mother and child generation after generation, in addition to any negative dietary habits the parents have, the child develops leaky gut syndrome.

Not all carbohydrates are harmful for those with gut dysbiosis, leaky gut, or GAPS. There are carbs that our Paleolithic digestive systems have an easier time digesting, such as the monosaccharides (glucose, fructose, and galactose) and gentler fibers in fruits and non-starchy vegetables. Monosaccharides can be absorbed directly into the blood stream via the small intestine with no additional digestive action, providing energy and sustenance. The fiber in fruits and vegetables is different from that in grains and starchy vegetables (e.g. potatoes) and is easier for the system to digest. However, when first beginning the GAPS protocol, certain very fibrous vegetables (e.g. celery) should be avoided until the intestinal bacteria community rebalances itself and the pathogenic bacteria and fungi are reduced to some extent, because fiber can feed those pathogens if severe dysbiosis is still present. Complex sugars (disaccharides and polysaccharides) and grain fibers are much harder to break down and require the aid of digestive enzymes and/or culinary fermentation (e.g. souring grains) for complete digestion and absorption. For those with dysbiosis, this part of the digestion doesn't work properly or is not enough to get the job done. When complex sugars, starches, fibers, and grain brans do not get completely broken down in the upper part of the digestive tract they provide food for pathogenic bacteria in the colon where they release gases and toxins that cause inflammation, pain, and leaky gut.

CF and Leaky Gut Syndrome
Leaky gut syndrome, or increased intestinal permeability, is not a common term in the CF lexicon. But it should be, as more research is elucidating the importance of a healthy gut flora in CF as well as the hidden prevalence of leaky gut syndrome in the CF population. Research has shown that "the intestinal microflora of [CF] children is often abnormal due to massive exposure to antibiotics, and in addition their intestinal permeability is increased suggesting disruption of intestinal barrier function" and that "the disruption of the intestinal epithelial barrier is central to the pathogenesis of several inflammatory diseases. Interestingly, an increase in intestinal permeability has been reported in atopic dermatitis and IDDM, as well as in CF. These findings suggest that probiotics may contribute in several ways to the first line host defence to environmental challenges" [27]. In addition, research is finding that gut inflammation is very common in CF: "intestinal inflammation is another typical feature of CF and is much more common than previously thought. Recently, we reported that fecal calprotectin concentration and rectal nitric oxide production are increased in virtually all children with CF, suggesting that intestine is a target organ in CF and is constantly in an inflammatory state" [26]. As you have read, gut inflammation is a central part of the pathogenesis of leaky gut syndrome. Furthermore, maintaining a healthy gut microbiome via good diet and probiotic supplementation is essential to maintaining lung health: "our findings suggest that nutritional factors and gut colonization patterns are determinants of microbial development in the respiratory tract in infancy and present opportunities for early intervention in CF" [26]. From my communication with other CFers around the world, I've found that many of us are presenting typical symptoms of leaky gut syndrome (e.g. low IgA, high systemic inflammatory markers, Celiac's and Crohn's disease, chronic bloating and gas, achy joints and bones, food sensitivities, etc.) yet our docs are not fitting the pieces of the puzzle together. It is my belief that these symptoms are not atypical of CF. In the future, I believe modern medicine will be treating CF and leaky gut syndrome together, as two aspects of the same disease, and maintaining a healthy intestinal ecosystem will become a central facet of mainstream CF treatment. Let us hope the medical establishment is enlightened sooner rather than later.

Since essentially all CFers have some degree of carbohydrate malabsorption and leaky gut syndrome, the only way to fix this problem at its roots is to eliminate complex sugars and starches as well as other foods that exacerbate leaky gut, and to eat probiotics to restore a healthy gut flora. The Gut and Psychology Syndrome (GAPS) diet is the most comprehensive way to begin the healing process. I will explain more about the steps that need to be taken in the various other sections in my website. 



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[23] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811559/ 
[24] http://www.dovepress.com/airway-inflammatory-markers-in-individuals-with-cystic-fibrosis-and-no-peer-reviewed-article-JIR
[25] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1450222/
[26] http://mbio.asm.org/content/3/4/e00251-12.full
[27] http://www.ncbi.nlm.nih.gov/pubmed/17360077
[28] Gut and Psychology Syndrome. Dr. Natasha Campbell-McBride. 
[29] Nourishing Traditions. Sally Fallon.