Last weekend my sister Kenzie and I presented a workshop on ecological medicine, nutrition, herbs, and microbiome health at the Northeast Organic Farming Association - Vermont Winter Conference at the University of Vermont. The lecture was titled "Ecological Medicine: Maintaining Health and Treating Disease Through Stewardship of Your Internal Biome". We had a great turn out, over 65 people, and folks asked great questions and seemed really engaged! We even have requests to give workshops in other places as well! 

I recorded our lecture on audio and put it together with my gut dysbiosis chart graphic (which I handed out to the audience) as a Youtube video. The chart in the video didn't turn out so well, so please use the chart below as a reference instead. Enjoy it, and let me know if you have any questions. Let's continue the discussion!

It's been over 6 months since I've started a strict GAPS-like diet and I've decided it's time to start reintroducing foods. My digestive system is happy with the changes I've made and I am digesting really well. But I have had trouble keeping weight on and my lung functions have not improved. The reason I stayed so strict on the GAPS diet for so long was to see if I could correct my gut flora sans antibiotics, and if that would help improve my lung functions. It did not. 

I have a very heavy bug burden - the MRSA is always there ready to cause me a fever and an infection if I'm not on antibiotics all the time. I really tried to stay off the antibiotics (both oral and IV) for long periods of time. I tried a month, then two months, then three months. I felt like crap, but I convinced myself that I was benefitting my microbiome by trying to regrow the beneficial bacteria in my guts by taking a break from the antibiotics. But without the antibiotics, my MRSA infections kept getting slowly worse. My regimes of eating well, exercising diligently, taking herbs and supplements, and experimenting with enzymatic biofilm inhibitors certainly helped - they've helped A LOT. But I've just got too much MRSA down there, and the bacterial biofilm issue is something that no one has yet helped me address in any significant way. So while I am going to continue with my dietary, herbal, and supplementary regimes, I am also going to try being more aggressive with antibiotics this next year to see if this will help my lung function and my quality of life improve. Part of my willingness to be more aggressive with antibiotics is my new discovery that IV vancomycin has no impact on the gut flora, and therefore will not disrupt all of the hard work I've been doing to restore my intestinal microbiome to a healthy ecosystem. 

I do believe that if my MRSA wasn't such a nuisance, the GAPS diet would have had a greater impact on improving my lung health. That is why I think it is so important to rebalance one's gut flora at an earlier age, possibly before big bugs like MRSA and pseudomonas have taken hold. The healthier the gut microbiome, the healthier the lung microbiome, and the more resilient the entire body becomes to resisting infections by these nasty pathogens. More and more studies are showing that if our microbiome is dominated by a healthy and diverse ecosystem of beneficial bacteria, we become better protected from infection and colonization by all pathogens (colds and flus included), but especially the typical big bad CF bugs, pseudomonas and MRSA. Remember that Germ Theory is only a piece of the puzzle - we must also keep in mind the Hygiene Hypothesis. Just because a germ (e.g. MRSA) is in your environment does not guarantee you are going to catch it and become colonized with it. That depends heavily on the strength of your immune system, your diet, the species that make up your microbiome, and a number of other factors. There is an often-told story of a famous scientist who wanted to challenge the wildly popular Germ Theory in a public way, so in front of a lecture hall of students he chugged a glass of water laced with cholera. He claimed that his microbiome was healthy enough that he would not be susceptible to infection by the cholera in the water he just drank. And sure enough, he was right. He did not develop a cholera infection, proving that there is more to the equation than exposure = infection. So in my mind, a lot of CF medicine should be focused on infection prevention, but not just with good hygiene and contagion control. Infection prevention can be much improved by optimizing the health of one's microbiome, and this is where the most exciting new research is headed. This is what is going to revolutionize medicine. 

Tending the Garden
Although I am going to be willing to use antibiotics, including oral antibiotics, more often in the next year as part of my new experiment, I am also going to be focusing more closely on tending to my gut microbiome. By becoming more diligent and regular about eating and taking in more probiotics and well as prebiotic foods, I am hoping that I can rebalance my gut microbiome even when I am on oral antibiotics. I will do this in 3 ways: 1) by making sure to eat lots of probiotic and fermented foods, especially saurkraut and kimchi, 2) by taking particularly well-studied strains of probiotics like Lactobacillus rhamnonsus GG (i.e. Culturelle) as well as an effective multi-strain probiotic everyday, and 3) by including a number of prebiotic foods in my diet. 

In the last month I've slowly added back in a little bit of grains (rice, quinoa, and millet in some seed crackers I buy) and added potatoes back in. I've discovered that my I still cannot control my blood sugar when I eat straight-up grains (i.e. a side of rice), plus my guts don't like it, so I only eat grains if they're mixed in with something else, like a bunch of seed in my Mary's Gone Crackers (I'm addicted to those things). For some reason my blood sugar is much more controllable (using insulin) with potatoes than grains, so I've started to eat some of those when I want to eat a carby meal. And I've also added in unmodified potato starch (Bob's Red Mill brand) as a prebiotic supplement in all of my smoothies. Unmodified (meaning unheated, unprocessed, and raw) potato starch contains a huge amount of resistant starch, a kind of carbohydrate that is completely unabsorbable and unusable by us, but is fantastic food for probiotic bacteria living in the colon, particularly bifidobacteria which are very important for our digestive health and regulating the immune system. Supplementing with raw potato starch to help boost the probiotic populations in our colon is becoming a really popular topic right now in the Paleo and Ancestral Health communities right now, so I thought I'd just on the bandwagon and try it. Check out this article if you want to read more about this topic in the Paleo blogosphere. 

Since starting this change in my diet I have actually noticed a big difference in my energy levels. I have a lot more energy and get tired less often, even when I feel "sick". I feel more robust, and even when I get a fever my temperature is higher than it used to be a few months ago, which I see as a good sign because it may be that I have more energy now to really get a good, high fever going. I am gaining weight again. My stools are phenomenally regular and beautiful, and I have no adverse G.I. symptoms at all, not even a little gas. In the beginning when I started using the potato starch in my smoothies, I did see a little uptick in the amount of gas I had, but that subsided in a week or two. 

Prebiotics
Anyway, as part of my new experiment I am focusing more on prebiotics. But be aware that in the beginning stages of the GAPS diet, prebiotics are significantly reduced and it is advised to avoid them as much as possible. This is because in someone with severe gut dysbiosis, eating prebiotics can actually feed those populations of pathogenic bacteria that are causing the person such digestive problems. However, as the theory goes, once these pathogenic bacteria have been "starved out" by adhering to a strict GAPS diet for many months, it may then be a good idea to begin to add in prebiotic foods alongside probiotic supplements to repopulate the guts with beneficial bacteria and to provide those bacteria with the fodder they need to rebuild a healthy and stable microbiome. In fact, eating prebiotic foods like fibrous veggies or potato starch has actually been proven to be more effective at building populations of probiotic bacteria like bifidobacteria in the colon than taking supplemental probiotics in pill form alone. However, I think the most effective strategy is to eat prebiotic foods and probiotic foods and supplements together, once the beginning stages of the GAPS diet have been completed. Again, every body is different, so the length of time one needs to stay on the strict GAPS diet and the way one begins to transition off the GAPS diet will look different for everyone. 

So far I have liked the results of my new strategy, and I will continue to keep you updated on any changes or improvements I experience. 

There is a storm of new info and research right now on the critical role that our gut microbes play in all aspects of our health, including our mental health. A recent article in Scientific American briefly summarizes a few key points and studies about how the lack of beneficial bacteria in the guts leads to depression. Click here for a link to the article. 

A lot of CF folks deal with depression at least occasionally, and it may not be solely from the difficult life situations we have to deal with - it's also caused by an imbalance in our gut flora! For more info on the gut-brain connection, read Gut and Psychology Syndrome by Dr. Natasha Campbell-McBride. She's been working in this field for years. 

The emerging understanding of the critical role that microbes play in our health is going to revolutionize the way we understand disease, and turn modern medicine on its head. Below is an article from my favorite science magazine, New Scientist. 




Why We Need Ecological Medicine
We know which species make us sick, but we must learn which species make us healthy.
By Rob Dunn

It was a revelation. Germs cause disease. When Louis Pasteur and Robert Koch discovered and developed what would later be called the germ theory in the 1860s, this was a radical, then revolutionary idea—one so good it seems obvious in retrospect.

At the heart of their work was the notion that individual species cause disease by invading our bodies. Over the next century, the notion of "germs" changed our behavior. It led us to scrub our hands and actively fight specific pathogens (as researchers came to call dangerous germs) and to cure the diseases they cause. These changes saved millions, maybe billions of lives. Every day you rub shoulders with the success of this theory. How could there be anything wrong with it?

New research, however, is beginning to question, if not germ theory itself, at least some of the actions we have taken on its behalf. These studies come from very different groups of scientists, largely working separately and apparently without much awareness of one another. But I believe that they are unwittingly part of the slow unraveling of a new, broader theory of disease, the ecological theory of disease.

Here's the thinking. In the late 1980s, microbiologists and public-health researchers began to notice differences between rural and urban kids. Rural kids seemed less likely to develop allergies. A new idea was floated—perhaps they had been exposed to more bacteria that had helped their immune systems to "balance" themselves. This idea, often called the hygiene hypothesis, has since found support in empirical studies worldwide.

Country kids whose fingers still plunge regularly into the rich bacteria of soil (and farm animals) have fewer allergies. But it isn't just farm living: Sometimes the exposure to a wilder bacterial life can be subtle. For example, a recent study in Australia found that pregnant mothers living with dogs were less likely to have children with allergies. These studies note fundamental differences between the immune systems of dirty kids and clean kids. Conclusion: In some ways it is better to be dirty.

More recently, a new version of the hygiene hypothesis has suggested that it isn't just large numbers of bacteria that it is good to be exposed to but, rather, many kinds of bacteria. Our immune system needs to be exposed to many species in order to sort the good from the bad. Without such exposure, argues this "biodiversity" version, mistakes get made. The immune system, in not having seen enough of the world, doesn't know quite what to attack. It attacks pollen. It attacks us.

This made me sit up and take notice. There are, I realized, many separate fields of science in which the failure to be exposed to good species or even just a diversity of species is believed to make us sick.

The "worm hypothesis" argues that our bodies evolved with parasitic worms as a dependable presence, and that for some individuals the absence of such worms causes the immune system to overreact, leading to autoimmune diseases such as Crohn's, multiple sclerosis, and asthma. The nature deficit hypothesis, on the other hand, argues that lack of exposure to nature in our city environments causes psychological problems in children who then suffer from any of a variety of behavioral and other problems. This is country cousin to the biophilia hypothesis, which suggests an innate fondness for nature and biodiversity, which both bring us benefits and, in their absence, costs.

All of these relate to the much older and well-accepted "deficiency" model, which correctly states that diseases such as scurvy are caused by the absence of whole classes of species (and their nutrients) in our diets.

What seems to have gone pretty much unremarked is that these ideas all suggest ways in which the absence of beneficial or historically common species in our lives can make us sick. In a way, taken together these ideas make up the obverse of the germ theory of disease; if the germ theory is about bad species being present, these hypotheses are all about good species that have gone missing.

Bringing the pieces of the puzzle together seems to show what I call the ecological theory of disease. This is the idea that illness can arise from the presence of species that negatively affect our health or the absence of species that positively affect our health.

Of course, to ecologists and evolutionary biologists, such a theory is not exactly news. We can all hold up long lists of species that require other species, their partners and neighbors, to survive. Think corals, lichens, leaf-cutter ants, tube worms, bean plants. Now think humans. Take away the species we benefit from every day and we would die in many different ways.

The point is that public-health researchers, medical researchers and doctors don't think like ecologists. Hospitals only consider other species when they are "bad," when, that is, they are behaving as germs. With a couple of examples we tend to regard as freakish (the medical use of leeches or fly maggots), doctors almost never prescribe the apple, bacteria, worm, or other sort of "nature" your body is "missing," though if you took just the right mix it would surely help keep the doctor away.

So what should we do? If the germ theory of disease tells us to hunt down, scrub off and otherwise avoid bad species, the ecological theory of disease suggests the same, but that we also need to figure out how to attract, farm, and nurture beneficial species. Fine. But there is a big problem: While we have spent the last 200 years chasing down bad species, we have spent far less time hunting good ones. Worse, while there are hundreds of pathogens that affect our health and well-being (with a small handful being the really deadly monsters), the precise mélange of beneficial species we need could involve hundreds of thousands of species—or more.

Those species do not always have names. Recently, I cataloged the species on my body and my house, finding more than 2,000 species, most of which most experts could not identify. Which ones were good for me? Who knows? What is worse, no one could tell me which good species I might be missing.

More and more, we seem to "know" that we need nature. Many of its species benefit us, but we are not yet smart enough to know which ones. We are left to wait for the systematists—those catalogers of life—to find and name the species on our behalf. And then we will have to wait some more for the ecologists and evolutionary biologists to study those species. Only then, finally, will medical researchers begin to weigh up which ones we need and which ones we don't. But it will take a while.

We have neglected the book of life for so long that at our current rate of research, without investment in projects larger than any yet imagined, much less implemented, we won't catch up for hundreds of years. Meanwhile, some of the species we are losing from forests and wild lands (or just from our modern lives) could easily be the ones that help to make us whole.

If we only knew which ones.

This article originally appeared in New Scientist.

Rob Dunn is the author of The Wild Life of Our Bodies, the story of our changing relationship with predators, parasites, mutualists, commensals, and all the rest. He is a science writer  and scientist  at North Carolina State University, where he studies the stories of the species that have lived alongside humans as we have spread around the world, be they bacteria in your belly button ants in your backyard  or cave crickets in your basement.