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The microbiome: What's it saying?

Updated: Apr 3, 2023

"Your Function or Disfunction is determined by the billions of organisms in your gut."

-Jennifer Luammen DVM MPH

In my last blog, I talked about the importance of the gut and how the health of your digestion system has a direct link to the rest of your body on how it feels, functions, or can cause dis-ease. Today, I want to dive in a little deeper and talk about how your specific microbiome in your gut plays a huge role in how our whole body performs; and provide insight on the new Cystic fibrosis studies that identify some of the issues CF individuals face within their microbiome and what I have found helps to create balance in a unbalanced environment.

Whoa-Symbiotic relationships with what?

The microbiome is a "collection of microbes that live in and on the human body and known as the microbiota.[1] The microbiome refers to the complete set of genes within these microbes." (1)

Since you were born you have been gathering, growing, and exchanging bacterial organisms between every thing you come in contact with. Each person is made up of their own diverse and unique microbiome (as unique as your fingerprint) that they have been collecting since they came out of the birth canal. One could say we are more bacteria than we are human as we have more bacterial organisms living within us and on our skin than the number of cells we have in our body.

According to Dr. Group at the Global Healing Center, we have "bacteria making up the bulk of the microbiome—about 30-50 trillion cells. The human body itself contains about 37 trillion human cells. It may be disconcerting to think of yourself as mostly microbial cells, but, by weight, you’re definitely mostly human as microbial cells are significantly smaller than human cells."

These organisms within our body communicate with other bacteria in our environment, people we come in contact with, and even with the food and other pathogens that we ingest. All of these factors have a impact on the type and diversity of the bacterial organisms that make up our unique microbiome.

These organisms in our gut usually carry on a symbiotic relationship with us, where we each help the other in survival. Our gut microbiome helps us break down and digest our food, it creates waste products that help absorb minerals in the body or remove toxins out of the body, make vitamins, and even determines our overall metabolism or energy production within the body. Some protect us from sickness and others if they get out of balance can become pathogenic and work against us causing illness.

The answer to living a healthy lifestyle is creating a environment that helps the good bacteria in your microbiome or the opportunistic flora of the gut thrive and keep the pathogenic bacteria (out of balance pathogens) that we come in contact with under control, it is the balance that is key.

What's Destroying the balance?

As you grow, develop, and change, so does your microbiome. It is constantly changing based on it's environment which we can control. We make changes within our microbiota with our own hygiene practices, the environments we live and surround ourselves in, and with what food we choose to consume, are very lifestyle can make all sorts of changes in our microbiome and body.

"You rely on your microbiome for many processes, including digestion and immune system function; the stronger it is, the better off you’ll be. (1)"

The opportunistic or good bacteria in our microbiome are the ones that we must feed the most as they are the defenders in our bodies and control the pathogenic bacteria and viruses within our bodies. If they are all over taken, killed or depleted the pathogenic bacteria, yeast, and viruses can take over. This is where illness and chronic disease can start to control your life and the way you feel, function, and absorb the necessary nutrients to survive.

This is where Cystic Fibrosis individuals have the biggest challenge and with the way our westernized diets are currently, what most individuals will become to know if we continue down the path we are on. The three most influential causes of increased pathogenic bacterial growth in our bodies are due to the following.

1.) Diet:

Diets consisting of large amounts of refined sugar and processed carbohydrates from pre-packaged processed foods.

These feed the pathogenic bacteria and yeast (Candida) in our bodies, creating food for there continued survival.

2.) Over use of Antibiotics:

Even if you don't go to the doctor all the time and take antibiotics when your sick, most of our food we consume contains antibiotics. The animals were either fed or given antibiotics during their lives that is passed on to us in the eggs, meat, and dairy products we consume and absorb. This allows the pathogenic bacteria in our bodies to create resistant biofilms around colonies of bacteria that become antibiotic resistant and hard for antibiotics and our immune system to attack and kill.

3.) Reduced Autophagy:

Reduced autophagy is the inability for our bodies to clean and repair the bodies cells effectively because our gut health is so reduced that leaky gut has become a problem. Therefore toxins, wastes, & large food particles are entering the blood stream and the lymph system causing chronic problems and chronic disease.

With Cystic Fibrosis (CF), these three items go hand in hand on what we have to deal with on a constant basis. When you have a delicate CF individual with a reduced immune system, a genetically dis-functional digestion system, and a body system colonized with pathogenic bacteria, it becomes a constant vicious cycle of exacerbations with a brief lapse in healthiness. If we do not know how to control the colonized bacteria in our bodies and repair our gut after several rounds of high doses of IV antibiotics or a round of oral antibiotics, we will remain in a constant state of disease.

CF Microbiome: FEV1 & Microbe Diversity

There are a few studies that have been done to see what kind of microbe diversity is in the CF gut and how IV antibiotics directly or indirectly affect gut health and lung function. Although scientists are just beginning to perform research on the CF microbiome, there are positive and negative outcomes that have been found.

One study conducted by Cork University Hospital, showed that the increased use of antibiotics had a negative correlation in the diversity of the gut microbiome. The more antibiotic courses that the CF individual had in the last 6 months caused a increase in the number of alterations to the microbiome diversity, causing a decrease in Bifidobacteria species and an increase in Fermicutes species. Bifidobacteria's are the solid defenders of the large intestine and actively synthesize vitamins and minerals in the gut. Fermicutes are the sugar burners in the gut. (2) Both of these depletion's in diversity would make sense considering we have weakened immune systems, trouble absorbing vitamins & minerals, problems metabolizing fats, and prone to insulin resistance or diabetes. All of which could be potentially linked to the diversity of microbes in the gut and overall gut health along with other factors of CF.

The study goes on to describe a positive correlation being found between % predicted FEV1 lung function and gut microbiota diversity, which has never been identified before.

"This is the first time that such a correlation has been reported. Percentage predicted FEV1 is used as a marker of lung function and therefore is used to track lung disease progression. As lung disease progresses, increased antibiotic exposure is almost guaranteed and so a collateral decrease in gut microbiota diversity is not surprising. However, identifying such a correlation presents a potential opportunity to use % predicted FEV1 as a marker, not only for lung function, but also as an indicator of gut microbiota diversity."

They also stated that, the "gut microbiome may help shape the development of the lung microbiota. Using such information could enable measures such as probiotic and/or prebiotic therapy to be applied to help minimize the decrease in gut diversity, thereby minimizing the associated negative health effects." (2)

I have found that probiotics and prebiotics are what has helped me to find the balance within the unbalanced system. Learning and maintaining my gut health has helped my daily CF symptoms to reduce and improve by a lot. I can't say that it has completely stopped all symptoms, but it has made changes in my daily quality of life. I don't have as many violent coughing attacks, I am absorbing my nutrients better and gaining weight, and my energy and focus is ten times better than it was as my adrenals are getting a much needed break and not overly stressed from constant inflammation. My lungs are also not tight from inflammation and I feel like I can take a deeper controlled breath than I use to. My endurance has also increased. Six months ago, I could barely make it up the six flights of stairs to my apartment without being short of breath and having a violent coughing attack once I made it to the top. So, for me maintaining my gut health is going to be a big part of my daily lifestyle. Repairing and building the terrain that will help your gut thrive is allowing yourself to control the balance within your whole body, meaning not only physically taking care of your body but also taking care of your emotions.

Controlling the Balance within!

To create an environment that allows the good bacteria to thrive takes some finesse and adjustments that are unique to the individual, but there are some basics that one can do to ultimately create a positive terrain within your gut, so the good bacteria come and stay. Below are the practices that I have implemented and they have created amazing changes in my overall health and energy.

1.) Movement:

This is more than just exercising to get a good cardio workout, which is also definitely a good practice to implement as well. For what I am talking about, I mean practice that moves your whole body, stretches the joints, and moves the stagnant lymph in your body. Practices such as Yoga, Gigong, Tai Chi, or Ecstatic dance that not only help stretch and move your body, but also allows you to address the emotional aspects within your body. Emotionally these practices allow for a type of meditative practice with a physical activity which helps to relieve stress, remove excess stagnant energy, stretch the body, and move the lymph fluid through the lymphatic system in the body creating a wonderful detoxification. I absolutely LOVE ecstatic dance, it frees my spirit and my mind of the daily stress while providing a beautiful detoxification through physical activity. I encourage you to check one out in your community.

2.) Probiotics:

Probiotics help to increase the good bacteria in your gut to help fight off bad pathogens and maintain gut health. Look for brands that have multiple strains of bacteria and not just one, examples would be Bifidobacteria, Lactobacillus, and Saccharomyces boulardi. Start with a small dose and work your way up to at least a therapeutic dose for adults of 15-20 billion bacteria cells a day (3). If you have die-off symptoms or feel sick then reduce the dose. Depending on severity of gut health you may just need a month or two of probiotics or you may need a on going dose if you have a chronic disease like CF. For me, I found that taking probiotics while on antibiotics helped tremendously on keeping my gut healthy and maintaining my immunity longer. I take them four hours after every oral antibiotic dose and when not on oral antibiotics, I take a 30 day course every other month for six months is recommended. It's also best to take this with food or just after, so the probiotics survive the stomach acid.

2.) Introduce Prebiotics and Resistant Starch:

These are the soluble fibers and starches that will feed the good bacteria and not the bad bacteria in the gut. These include potato starch, taro root, yuca or tapioca starch, plantains or unripe bananas, jicama. You can also find good prebiotic powders at the health food store or within your probiotic.(4)

3.) Eat grains & fruits high in sugar in moderation:

This is most important when you have just finished a antibiotic course as that is when the (yeast) candida in the body likes to move in and take over because all the pathogens are gone. Minimizing these foods will help control the overgrowth because you will be starving it.

4.) Take trace minerals & multi vitamins:

Most individuals especially those with CF are lacking in all of these essential minerals and vitamins, especially magnesium and vitamin D. I like Youngevity plant derived trace minerals. These are great mixed in smoothies or a green juice as they don't particular taste good by themselves in water. Or use cold infusions of Stinging Nettle herb and Oatstraw for more vitamins and a hot infusion of them for more minerals. Infusions are teas steeped for 4 to 6 hours or more, make them in the evening to enjoy in the morning and throughout the day.

5.) Drink Pau de arco tea & take Sacchromyces boulardi:

After antibiotic doses to help control the yeast overgrowth. I drink one cup of Pau De Arco tea daily for two weeks along with the Sacchromyces boulardi which is usually a 30 day course. If you have been on a lot of antibiotics you may want to do three weeks of the tea. These are the ones I like Renew Life and Traditional Medicinals teas.

6.) Use botanicals & herbs as maintenance antibiotics:

To control colonized bacteria and reduce the risk of antibiotic resistance.

This is a delicate one as everyone has a different gene makeup and different herbs will work or not work for different people. It is a trial and error and one should work with a Natropathic doctor to determine which botanicals may work best for them along with their CF doctor. I like to use Garlic, Oregano oil, Usnea and Elecampane as these have worked the best for me. I have tried Cryptolepsis to help with my MRSA as this is susceptible to this, but I found Oregano oil to work better and more readily available. There are plenty of plant books that can assist you as well in learning about natural medicines and different pathogens, my favorite one is Antibiotic Herbs.

7.) Try the Gut Thrive in 5 program from Whole Journey to pathogen purge and heal the gut.

The Whole Journey website has a wealth of knowledge about gut health, bacteria, and how food can be your best medicine. They have terrific products, programs that you can look into to heal your body, and fantastic recipes!! I am doing this 11 week Gut Thrive program right now, and I feel beyond fabulous!! To check it out click here.

8.) Drink Green juice everyday:

For me this has been the game changer in my overall energy. As CF individuals, our liver and adrenals are constantly working overtime to remove the toxins from our bodies. With CF, this can be challenging as the liver doesn't always like to work properly, so we can get adrenal fatigue and die-off detox symptoms pretty easily. I have found this to be very true throughout this journey of healing and the green juice has made all the difference in the world. Eating greens is one thing, but I have found that the green juice with one fruit or less is the perfect way to boost my energy. The green juice is full of Magnesium which is the number one mineral for helping to remove toxins from the body, and I am usually low in this vital mineral. Here in Hawaii, Whole foods makes a great one, and it's only $15 bucks for a big jug. Made with Lemon, Mint, dandelion greens, kale, celery, & spinach, but it's also easy to make your own at home.

9.) Drink Tumeric/Ginger lemonade or tea:

As often as possible to help reduce inflammation in the body. This is another item that has helped me a lot in making my lungs feel clearer and not so tight.

I make my lemonade from scratch, but they do sell tumeric/ginger teas at many health food stores if that is more your route. The most nutritious would be boiling the ginger and tumeric roots themselves for about ten minutes to get a real medicinal benefit from these amazing healers and then strain the tea. If you can't find the roots at your grocery store, you can find them in the spices usually, but the root will have more nutritional benefit as it is not processed. The tea can be then made into lemonade or just drank as tea.

10.) Introduce Gut Healing Foods:

High quality bone broths like Kettle & Fire, Pacifico, or make your own. Greens wonderful greens like chard, cabbage, spinach, kale, collard greens, etc. Omega 3 fats like in coconut, wild fish, and some nuts (walnuts, almonds, cashews, macadamia nuts, brazilian nuts), organ meats like liver are full of collagen which is great for healing the gut lining. If your not a liver fan, you can use collagen powder in soups or smoothies instead.

These are just some of the changes that I have introduced into my daily lifestyle and even though it has only been almost a year since the start of it all, I can honestly say that my health and quality of life have already changed dramatically for the better since my health decline in the beginning. It was hard at first to make all the changes with such low immunity and weakness, but small changes everyday made a drastic impact in the long run. Before I knew it, most of these had just started to be a habit after awhile and now I hardly have to remind myself. The best rule I can give you is incorporate the 80/20 rule and if you slip up or forget something, don't stress just let it go and begin a new tomorrow. So, I encourage you to try something new everyday or every week whatever works with your lifestyle and keep on moving forward to a bright and beautiful healthy you!

Eventually, these changes will fall into place as habit and you will start to feel ten times better. Your body, mind, and spirit will thank you in the long run and so will your gut microbiome.

I would love to hear what new items you tried or any comments, suggestions you may have in the comments below.

As always with lots of Love & Aloha.



  1. Dr. Edward Group DC, NP, DACBN, DCBCN, DABFM. "Gut Health 101: What Is the Microbiome?" Global Healing Center. Dec. 22, 2016. Viewed on 5/28/18. <>

  2. Burke, D.G. et al. “The Altered Gut Microbiota in Adults with Cystic Fibrosis.” BMC Microbiology 17 (2017): 58. PMC. Web. 29 Apr. 2018.

  3. McBride-Campbell, Natasha MD. "Gut and Psychology Syndrome." 2010.

  4. Christa Orecchio & Jack Tips. "The Ffve Steps to Gut Healing." The Whole Journey webinar. 2015. The Whole Journey Website. Viewed 5/7/2018.<>

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