SIBO Part 2: How Bone Broth Helps

SIBO Part 2: How Bone Broth Helps

In this blog we’re discussing how bone broth helps SIBO symptoms. If you’re unsure what SIBO is, check out Part 1 of this blog, found here! 

We know from Part 1 that SIBO can be a complex disorder, resulting from one or more of multiple causes and connected with other chronic health conditions. Treatment for SIBO involves addressing the SIBO itself, as well as addressing the specific cause(s) of SIBO. This is the only way to prevent SIBO from recurring. There are many supportive nutrients that help ease the symptoms of SIBO and can be included as part of treatment. One such support is found in bone broth.

Bone broth is made by simmering animal bones, usually beef or chicken bones, along with vegetables and spices, for several hours. The nutrients in these ingredients are leached into the water, creating a flavorful and nutritious broth. Bone broth is packed with various nutrients including several vitamins, minerals, and collagen. Drinking bone broth regularly helps support our health in many ways. 

The collagen (specifically type II collagen) serves to protect our joints from the stress of continual use and increase bone density in post-menopausal women. It can also improve joint stiffness, pain, and joint function in those with osteoarthritis. Type I and type III collagen help improve skin hydration, elasticity, and minimize appearance of wrinkles. The amino acid, glycine, found in collagen, may improve sleep quality, regulate our circadian rhythm, and minimize fatigue during the day. 

More than this, bone broth supports digestive health and promotes gut healing, making it a wonderful health drink for those with gastrointestinal problems, such as SIBO (small intestine bacterial overgrowth). Be aware that most commercial bone broths may cause worsening symptoms for those with SIBO. To avoid this, it’s important to modify the bone broth in a couple of ways. Let’s discuss SIBO and bone broth, as well as how to alter bone broth for better gut tolerability. 


How Bone Broth Helps SIBO Symptoms

Bone broth contains several minerals and vitamins that are easily digested and utilized by the body. This includes magnesium, calcium, zinc, iron, phosphorus, and vitamins A and K. These nutrients are more easily absorbed than when they are found in food, making it easier for people with SIBO to get the nutrients they need. 

Most of the gut-healing properties of bone broth, however, are found in another type of nutrient: Collagen, specifically type III. Collagen is a structural protein containing 19 amino acids, with particularly high amounts of glycine, proline, and glutamine. Collagen is found in our skin and connective tissue, including our digestive tract! The amino acids in collagen help heal the lining (or wall) of our intestines (“gut”) and stomach. Glutamine, a very common amino acid and one that is found in bone broth, is well known to heal “leaky gut syndrome” by preventing the inflammation of our gut lining. 

Leaky gut is a common occurrence in those with SIBO and can lead to bloating, gas, diarrhea, constipation, IBS, food sensitivities, and more. Repairing a leaky gut lining can ease these symptoms, which cause the most discomfort for those with SIBO. Collagen also regulates stomach acid, ensuring the proper amount is released to avoid heartburn and help with digestion. 

With regards to other SIBO symptoms such as depression, anxiety, and brain fog, bone broth is here to help. The connection between our gut and our brain is well established. Our mood and mental state is directly impacted by the health of our gut. By improving our gut health, bone broth indirectly improves and balances our mood and ability to focus.

Keep in mind that it is best to use bone broth for supplemental collagen only, and not to replace it with any part of your SIBO treatment. This is because the amount of collagen and amino acids found in bone broth vary greatly depending on several factors, such as the type of bone, the number bones, the type of animal, and how long the broth simmered. These factors can cause collagen amounts to range from 2.5 to 11.5 grams per serving of bone broth. Furthermore, the amount of collagen in bone broth is rarely listed on the label, so it is impossible for the consumer to know exactly how much collagen they are getting. Therefore, if you are needing specific amounts of collagen or the amino acids found within it, it is best to obtain them from supplements to maintain consistency.


Not Just Any Bone Broth Will Do 

Conventional bone broth on store shelves may cause digestive discomfort for those with SIBO. This is due to the cartilage in the bones, as well as the various high FODMAP vegetables used to flavor the broth. Luckily, there are great work-arounds! Bone broths can be made-to-order, thereby removing high FODMAP ingredients. There are also ways to get the right kind of bones that don’t contain cartilage, so you can make bone broth at home.


Ingredients To Avoid 

Conventional bone broths (or any broths) often contain high FODMAP vegetables such as onions or garlic that are added for flavor. Even though they’re removed from the broth, the “oligosaccharides” (which is the “O” in FODMAP) have already leached into the liquid, making it a high FODMAP broth. Those with SIBO should avoid any broths that list garlic and onions in the ingredients. Avoiding onions and garlic in bone broths can be tricky. Beth’s Bountiful Bone Broth is a locally-owned business in the Columbia Gorge that offers high-quality bone broths that can be made-to-order for your low FODMAP needs. 


Beth makes a veggie pre-mixed spice kit containing dehydrated vegetables and spices for your homemade bone broth. Just add the bones! Alternatively, you can omit the bones and simply simmer the beef or chicken meat for a thinner broth. This veggie spice kit already contains garlic and onions unless specifically requested otherwise. Contact Beth to request a low FODMAP spice kit and she will make one just for you, without adding onions and garlic. Instead, this low FODMAP spice kit will contain air dried carrots, celery, shiitake mushrooms, turmeric, peppercorns, and various dried spices. Not only do these enhance the flavor of your homemade bone broth, but it also provides health benefits from the shiitake mushrooms and turmeric. Shiitake mushrooms help in lowering cholesterol, strengthening the immune system, lower diabetes risk, and help with eczema. Turmeric spice is a powerful antioxidant, anti-inflammatory, and antimicrobial. 


The Type Of Bone Matters 

Avoiding onions and garlic in your bone broth is just the first step towards making it low FODMAP. The types of bones used to make broth should also be considered. Most conventional broths are made using bones that have cartilage attached to them. Cartilage is the connective tissue that protects joints and is found where two bones join together. To make broth, these bones are boiled in water for several hours, releasing a type of carbohydrate (called monosaccharide) that is high FODMAP. In fact, monosaccharide is the “M” in FODMAP, and it’s released into the water during boiling. This results in a high FODMAP broth and should be avoided by those with SIBO.

So what’s the solution? Low FODMAP bone broth must be made using marrow bones, or long bones, without the connecting cartilage. Marrow-based broths are safe for those with SIBO and do not cause gut symptoms. However, don’t expect to find marrow-based broths at the grocery store. Most brands will not indicate which type of bone was used; even organic bone broths will not state this. In fact, unless specifically stated that marrow bones were used, it is best to assume that they aren’t good for SIBO. 

If we can’t trust conventional bone broths to use marrow bones, what are our other options? Usually, people with SIBO would need to make their own broth instead. It is possible to find marrow bones at your local beef ranch by calling ahead and asking if they would sell you some. To get the most out of the bones, make sure the ranch uses organic growing practices and raises grass-fed beef. If you have trouble finding a local ranch, you can always purchase online. Seven Sons Ranch and Oregon Valley Farm both sell marrow bones online and ship within the U.S. 

Unlike beef bone broth, chicken bone broth cannot be made low FODMAP, even if made at home. This is because chicken bones contain much more cartilage than beef bones. Further, there are far less marrow bones on one chicken carcass, meaning you’d need to source bones from multiple chickens in order to achieve the right flavor profile. This is not usually feasible. The best way to enjoy chicken broth if you have SIBO is to make it without any bones (or onions and garlic). 

Making broth without bones is always an option for those with SIBO. Simmer beef or chicken meat instead, making sure to avoid onions and garlic! 

However, if you don’t want to make anything yourself, then we recommend the grass-fed beef bone broth, which is made with marrow bones. This is liquid bone broth already made and ready to enjoy! It does contain garlic and onions, however, so be sure to call ahead and request a low FODMAP version. 


A Personal Story

Beth Kandell, owner of Beth’s Bountiful Bone Broth, has had her own experience with SIBO and how drinking bone broth has helped calm her symptoms:

I have had SIBO for many years. I actually cycled through all three types! Methane-dominant, then hydrogen-dominant, and then mixed. I had all the classic gut symptoms and couldn’t get them under control. I would also always wake up extremely hungry in the middle of the night! I was already taking the usual herbal supplements for SIBO treatment, but I decided to add in  some bone broth (without onion or garlic). I drank a cup of broth during the day and another cup before going to bed. What a difference it made! My digestive symptoms calmed down and I felt much more comfortable. Best of all, I began sleeping through the night again! My nighttime hunger gradually began disappearing until it was no longer an issue. Of course I kept taking the herbal supplements, as prescribed for functional healing, but I credit the bone broth for the noticeable difference in my symptoms. It gave me back my life (and sleep)!

SIBO Part 1: Causes and Symptoms

SIBO Part 1: Causes and Symptoms

SIBO (Small Intestine Bacterial Overgrowth) is a very common digestive disorder that produces a variety of gastrointestinal symptoms. Those with SIBO are often first diagnosed with IBS (Irritable Bowel Syndrome), which shares much of the same symptoms as SIBO. In addition, there are other symptoms associated with this disorder that are not related to the digestive system. SIBO has multiple underlying causes and is linked with other chronic diseases. As such, SIBO is the end result of other health conditions. It is what can happen when chronic health issues go unaddressed.

Treatment usually follows a foundational protocol that is then added to depending on the unique cause of a persons’ SIBO. There are several supportive nutrients that can be included in SIBO treatment. Bone broth is one such food item that supports health in many ways including digestive health and gut healing. The benefits of bone broth and how it can help heal SIBO is discussed in part 2 of our SIBO blog. Be sure to check it out since conventional bone broth contains ingredients that make SIBO symptoms worse. Our part 2 blog describes ways to get the right kind of bone broth.

So, what exactly is SIBO and what symptoms should I be aware of? Let’s dive in to find out!


What Is SIBO And How Is It Diagnosed?

One of the most common chronic symptoms that millions of Americans struggle with are digestive symptoms. This ranges from bloating, gas, diarrhea, constipation, or just general abdominal pain. These symptoms are identified in a number of digestive disorders to varying degrees. Let’s discuss one such disorder, called SIBO (Small Intestine Bacterial Overgrowth).

SIBO is when certain species of our gut bacteria migrate to and populate our small intestine (where they don’t belong). Gut bacteria is normally found in our large intestine, but when they travel to our small intestine they can cause several unpleasant digestive symptoms. More than that, the misplaced gut bacteria disrupt the normal functioning of our small intestine, namely nutrient absorption. This can lead to deficiencies in several nutrients.

You may have heard it said that anything that affects the gut affects the rest of the body. Our digestive system is integrally connected with every other body system. For this reason, SIBO is linked to other health conditions. These include rosacea, psoriasis, fibromyalgia, chronic fatigue syndrome, hypothyroidism, rheumatoid arthritis, other digestive disorders, and many more. These health conditions either predispose people to SIBO, are caused by SIBO, or are co-existing conditions. If you are struggling with a chronic disease, it would be wise to get tested for SIBO and any other gut abnormalities.

SIBO is diagnosed using a breath test after fasting for 12 hours and then drinking a sugary solution (lactulose). Breath samples are collected throughout the day using a take-home kit and then analyzed for the presence of hydrogen and methane gases. These gases are produced by the overgrowth bacteria as they ferment the lactulose drink. People are diagnosed as having methane-dominant SIBO or hydrogen-dominant SIBO. Some can have a mixture of both gases, while others can have hydrogen-sulfide SIBO.


What Causes SIBO?

SIBO can be caused by a number of factors. Most people actually have several factors compounded at once. It’s important to learn what has caused your SIBO so that your treatment can be modified to address and reverse the cause.

Low Stomach Acid

A common cause of SIBO is low stomach acid. Low stomach acid can result from taking antacids or PPI medications, having chronic stress, having a bacterial infection called H. Pylori, or from eating inflammatory foods. Interestingly, an H. Pylori infection can result from relying on heartburn medication for several years. Both of these combined raise the risk of developing SIBO.

Low Bile and Digestive Enzymes

Another cause of SIBO is low production of bile and digestive enzymes. Bile acids help balance our gut bacteria and prevent overgrowth. Digestive enzymes digest carbs, proteins, and fats. If we aren’t digesting carbohydrates appropriately, they can feed our gut bacteria, causing them to overgrow. Having low stomach acid leads to low bile and enzyme production, putting us at increased risk for SIBO.

Impaired Gut Motility

Some people have slow or impaired gut motility (gut contractions). This means their digestive tract does not physically move food through the body in an efficient way. Food, and the natural bacteria on our food, will stagnate in our gut if it is not able to move through our system. If these aren’t cleared from our gut in a timely manner, bacteria can settle where it doesn’t belong and cause SIBO. Our gut motility can be impaired by hypothyroidism, proton pump inhibitors (PPI’s), diabetes, or even other digestive disorders such as celiac or IBD (inflammatory bowel disease).

Heavy Antibiotic Use

Ironically, SIBO can also be caused by the overuse of antibiotics. These medications kill off all bacteria, both helpful and harmful. In such a harsh environment, only the strongest bacteria survive. Oftentimes the strongest bacteria is the harmful type. Without the helpful bacteria to keep it in check, harmful bacteria are allowed to thrive and overgrow, causing SIBO. Another risk of taking antibiotics is that your gut bacteria may adapt to them and be unaffected by them. This is called antibiotic resistance and makes it even more difficult to treat SIBO and any other bacterial infection.

Other Causes of SIBO

There are other causes of SIBO including autoimmune conditions, gut dysbiosis, food poisoning, chronic stress, and leaky gut syndrome. Anybody who has a history of these SIBO causes should be treated appropriately in order to prevent SIBO from developing.


Symptoms of SIBO

Symptoms associated with SIBO can mirror the symptoms of other digestive disorders such as IBS. In fact, having IBS is a common precursor for developing SIBO, with about 60% of IBS patients also having bacterial overgrowth.

Common SIBO symptoms are bloating, gas, diarrhea, and constipation. A more complete list of SIBO signs and symptoms is below:


Food sensitivities
Leaky Gut Syndrome
Pain from bowel movements
Abdominal cramps
Feeling of fullness
Malnutrition and nutrient deficiencies
Weight loss
Brain fog


Not every person with SIBO will have each of these symptoms. In fact, SIBO affects each person differently and at different levels of severity. One person may have mild stomach cramping while another person may have debilitating cramps that take them out of work. Depending on the severity of symptoms, those with SIBO can have a lowered quality of life.

SIBO Treatment and Die-Off Symptoms

It was said earlier that SIBO is the end result of other health conditions. Thus, simply treating SIBO does not address these underlying conditions which allow SIBO to thrive. The root cause needs to be treated as well, to prevent SIBO from recurring. In this way, there are two parts to treatment: treating SIBO itself and treating the underlying cause. Each person’s underlying cause will be different, making each SIBO treatment unique.

Treatment for SIBO itself involves taking antimicrobial supplements that target and kill bacterial overgrowth. Many people also need to take a specific antibiotic, called Rifaximin, which works in the same way as the supplements.

Other than prescription antibiotics and supplements, those with SIBO should adhere to a low FODMAP diet for several weeks. This diet avoids certain carbohydrates that feed the overgrowth of bacteria. Avoiding these foods essentially starves them out and prevents them from growing. “FODMAP” is an acronym where each letter stands for a different type of carbohydrate that can be bothersome for those with SIBO. This is why a “low” FODMAP diet is ideal during the treatment process.

One round of SIBO treatment can be quite effective for people but some may require multiple rounds of treatment before the overgrowth is eradicated. If the underlying cause of SIBO is also treated, the odds of total eradication increase dramatically.

During SIBO treatment, many people experience a unique set of symptoms for a short time. The supplements, antibiotic medication, and specialized diet all act to eliminate harmful bacteria and bring the overgrowth back into balance. As harmful bacteria die, they release toxins into your body. These toxins cause a reaction, called a ​​Herxheimer reaction, or die-off symptoms. These don’t occur in everyone though, and they usually are short-lived. Symptoms of die-off include flu-like symptoms, muscle or joint pain, irritability, fatigue, and digestive symptoms (most commonly bloating). If people experience die-off symptoms, they often take certain supplements, as needed, that act as detox binders. These binders attach to the bacterial toxins and escort them out of the body, reducing symptoms.


We’ve seen how SIBO can develop and how it’s related to multiple other chronic health conditions. SIBO symptoms vary among people and range in severity. There are several factors that can cause SIBO and it’s important to identify the cause to help guide treatment. Treatment involves a standard approach along with specific supports unique to each person. Sometimes SIBO treatment can cause die-off symptoms that are usually short-term. In part 2 of our blog, we’ll discuss one of the ways to support gut health for those with SIBO. Check out part 2 here!

Link Between Autoimmune Disease and Our Gut

Link Between Autoimmune Disease and Our Gut

The impact that our digestive system and gut bacteria have on the health of our entire body goes largely unnoticed until a disease or other dysfunction develops. And even then, the link between the gut and the disease often goes unrecognized. After all, who would think to look at the gut when someone has multiple sclerosis? The truth is, however, that our gut has powerful influence over how well our body operates and is the number one underlying cause behind all chronic disease, including autoimmune disease. It’s important to note that ongoing gut dysfunction can occur even in the absence of gut symptoms. This is why it’s wise to look at the health of our gut and microbiome whenever there is an autoimmune risk or diagnosis. Let’s dive deeper into this connection.


How Our Gut Affects Our Whole Body


Let’s take a quick look at some of the ways in which our gut communicates with and controls various functions within our body:

Gut and Immune System:

It is said that our gut contains between 70% and 80% of our entire immune system! And when you think about it, it’s not all that surprising. After all, every time we eat food we’re introducing a foreign substance into our body and our immune cells must identify it as “safe.” Once the food item is deemed to be safe, the immune system continues its patrol, no longer paying mind to our meal. The harm occurs when our immune system becomes hyper-focused and marks something as a threat when in reality it’s actually safe. 

These immune cells interact with the bacteria in our gut and are sensitive to any changes in our microbial environment. Our gut can be prompted to “switch on” our immune system for short periods of time, such as when we’re fighting off an infection, or for long periods of time, which is unhealthy and leads to chronic inflammation and disease, including autoimmune disease. This chronic immune activation (always being switched on) lowers the ability of immune cells to distinguish between threats and non-threats. A hyper-focused immune system has many causes, with poor gut health being chief among them. 

Gut and Inflammation:

The lining of our intestine is designed to transfer nutrients from the food we eat to our bloodstream, where they’re carried into our body tissues. This lining is composed of a single layer of intestinal cells that are lined up tightly side-by-side (called “tight junctions”). These tight junctions are so tight that they can only allow small particles (micronutrients) into the bloodstream. 

However, if that tight cell lining gets loose (or “leaky”), larger particles escape our intestine and pass into our bloodstream. These larger particles include harmful bacteria, bacterial toxins, large proteins, and undigested food bits. Once these hit our bloodstream, our white blood cells (immune cells) recognize that they don’t belong there and launch an attack.

Anytime our immune system launches an attack (whether or not it’s justified), inflammation is always present. Acute inflammation is a healthy response and only lasts long enough for our body to fight off an illness. When the immune trigger (like a cold virus) is fought off, it leaves the body and our immune system calms down. However, when our immune system is constantly exposed to its trigger (such as food toxins, harmful bacteria, or our own body cells), then our inflammation becomes chronic, or ongoing, and can spread throughout the body. When the cause of the attack (such as a leaky gut) is ongoing (such as the unhealthy food we eat), then we get chronic inflammation. Chronic inflammation increases the possibility of autoimmune disease in those who are at risk. It can also tip the scales from having subclinical autoimmune issues to reaching clinical thresholds for diagnosis. 

Gut and Mood/Cognition: 

Furthermore, our gut bacteria impacts which neurotransmitters are made in our digestive tract (95% of our serotonin is made by our gut bacteria!). Neurotransmitters include GABA, serotonin, dopamine, norepinephrine, melatonin, and others. These chemical messengers collectively impact our mood, alertness, stress response, memory, learning, motor control, and digestive function. Similar to immune cells, the production of neurotransmitters are also sensitive to any alterations in gut bacteria. 

Gut and Brain:

Our gut is often referred to as our “second brain.” As we learned in school, our central nervous system (CNS) comprises our brain and spinal cord where millions of electrical signals are sent back and forth between our body and brain every second. Similarly, we also have an enteric nervous system (ENS) located within our digestive system that controls our gastrointestinal secretions, motility (peristalsis), local blood flow, and overall digestion. It also modulates our immune system and endocrine (hormone) responses. Lastly, the ENS interacts with our gut microbiome and the nutrients from our food. The ENS of our gut communicates with the CNS of our brain through a long nerve called the vagus nerve. This connection is what describes the “gut-brain axis” where any imbalance or dysfunction of our gut health is immediately broadcast to our brain.

Gut and Thyroid:

The thyroid helps control the function of our muscles, heart, digestive system, bone integrity, and brain development. This important gland uses a hormone called TSH, which produces two other hormones, T3 and T4. T4 is an inactive hormone and must be converted into T3, the active form. Our gut bacteria are charged with converting about 20% of all T4 into T3. This conversion can only happen, however, with a certain enzyme that is produced by healthy gut bacteria. Harmful gut bacteria, on the other hand, contain a toxin called LPS that reduces levels of thyroid hormone and decreases TSH (thus lowering production of T3 and T4). Furthermore, the T3 hormone can be reduced by constantly high cortisol levels caused by stress and gut inflammation. 


What Is Autoimmune Disease?


Autoimmune disease encompasses several diseases each sharing a common thread in their etiology (how a disease is caused). All autoimmune diseases are caused when the immune system mistakenly attacks the body. This is either because it can’t distinguish between normal body cells and foreign invaders, or because it can no longer control the intensity of immune response (ie it doesn’t know when to stop fighting).

During an autoimmune response, rather than producing antibodies against a harmful outside invader (such as the cold virus), the immune system produces autoantibodies, which are antibodies against “self”, thus marking our own body cells for attack. Where this attack takes place defines which type of autoimmune disease a person has. For example, an immune attack on the thyroid can lead to Hashimoto’s or Graves diseases, whereas an attack on the myelin sheath that protects nerve fibers can lead to multiple sclerosis. 

In America, about 23.5 million people have an autoimmune disease of some type. These diseases are more common in women than in men. Examples of autoimmune diseases include type 1 diabetes, rheumatoid arthritis, lupus, Hashimoto’s, multiple sclerosis, celiac, psoriasis, and IBD (inflammatory bowel disease which includes ulcerative colitis and Crohn’s). Some scientists are considering Alzheimer’s disease to be an autoimmune disease as well.

Researchers don’t fully understand why the immune system targets body cells, so there are no surefire cures to autoimmune disease. The cause(s) of autoimmune disease is also not fully known, but we do know of several contributing factors. These factors include genetics, family history, viral and bacterial infections, exposures to toxins, obesity, and eating a Western diet. As the title of this blog suggests, autoimmune diseases are also strongly linked to the health of our gut microbiome.


Gut Dysbiosis and Autoimmune Disease


As mentioned earlier, chronic inflammation is detrimental to our health and an instigator of disease. Such inflammation is brought about by ongoing immune activation. This hyperactive immune response can tip the scales towards autoimmune disease. And since the majority of our immune system lies within our digestive tract, the health of our gut is imperative to the health of our immune system.

Part of keeping a healthy gut involves maintaining healthy bacteria that live in our gut (specifically in our large intestine). In fact, it is our gut bacteria that are responsible for regulating the majority of our immune system. Thus, it is important to keep our gut bacteria healthy and balanced. An imbalance of gut bacteria (dysbiosis) can lead to an overreaction of our immune system and the propensity for mistakenly attacking our own body tissues leading to the development of autoimmune disease.

Having too many harmful or pathogenic bacteria in our gut can overrun the number of healthy bacteria, leading to dysbiosis. These harmful bacteria are pro-inflammatory and contain toxins that jeopardize the integrity of our gut lining. These insults (increased inflammation and a leaky gut) cause an inappropriate immune response.

What Causes Dysbiosis?

Gut dysbiosis is caused by a number of factors. The overuse of antibiotic medication wreaks havoc on our gut bacteria and causes a significant reduction in the diversity of bacterial species. Chronic stress slows the motility, or movement, of our GI tract, thus altering the composition of our gut bacteria species. Diets high in sugar and processed carbs and low in fiber are associated with lower diversity of bacterial species as well as higher levels of harmful bacteria. Toxins found in food such as PCB’s, dioxins, pesticides, and food borne chemicals produced in high-heat cooking, can all cause inflammation in the gut as well as an imbalance of microbiome functions and activity.  

Additionally, several of the contributing factors to autoimmune disease, discussed earlier, also threaten the balance and diversity of our gut microbiome. These include viral and bacterial infections, exposures to environmental toxins, and obesity.

Incidentally, all of the above causes of dysbiosis also cause inflammation, further perpetuating an improper immune response and a risk of autoimmunity. Note that these same insults can lead to other diseases that aren’t autoimmune in nature. 


Improving Gut Health To Address Autoimmune Disease


We have seen how out gut and our immune system are intertwined, and how the bacteria in our gut play a huge role in how well our immune system functions. We also discussed the impact of chronic inflammation and the role it can play in autoimmune disease. So, what do we do about it?

Is Your Gut The Underlying Cause?

The health of our gut and the balance of our gut bacteria is a common underlying cause of autoimmune disease, oftentimes occurring alongside other underlying causes. If you have an autoimmune condition, it’s best to determine the cause(s) and whether or not it stems from gut health. Our functional medicine team can look at the biodiversity of your microbiome to see how many bacterial species there are in total, as well as which species are beneficial versus harmful. Knowing your bacterial makeup so-to-speak, alerts us to any overgrowth of bad bacteria or yeast, as well as to any undergrowth of good bacteria. Lastly, we assess level of gut inflammation to see whether you may have “leaky gut” or intestinal permeability. If the health of your gut or microbiome is compromised, we work with you to restore balance, healing, and function. In doing so, autoimmune flare-ups or disease progression can be mitigated or even prevented.

Follow An Anti-Inflammatory Diet:

As with any chronic disease, the key to addressing autoimmunity is by first limiting inflammatory foods. Foods that cause inflammation are the usual culprits such as gluten, dairy, processed foods (including processed meats), refined carbs, refined vegetable oils, and sugar. Limiting or avoiding these foods, not as part of a diet but rather part of a long term lifestyle eating pattern, will lower inflammation throughout the body. This occurs as your immune system calms down in the absence of the onslaught of toxins it’s used to dealing with. A calm immune system is now able to attend to actual threats (like the flu) rather than exhaust all resources fighting off the byproducts of the food we eat. An anti-inflammatory eating plan will also encourage healthy growth and diversity of beneficial gut bacteria, while outcompeting harmful bacterial species. Bringing balance to our gut bacteria helps restore appropriate function to our immune system.

Anti-inflammatory foods are the key to calming down an overactive immune response. These foods include fruits, vegetables, legumes, whole grains, healthy fats, clean proteins, and fermented foods. There are many versions of an anti-inflammatory diet, and for those with an active autoimmune disease, the autoimmune paleo diet (AIP) is commonly followed. The aim of this diet is to reduce flare-ups and calm symptoms. To do this, the AIP diet eliminates not only inflammatory foods, but also several categories of anti-inflammatory foods. These include all grains, legumes, dairy, eggs, and nightshade vegetables. Following the AIP diet can be tricky and overwhelming at times. Our team at CustomCare Nutrition can help you navigate it successfully!

Heal The Gut:

As mentioned earlier, the lining of our intestine is supposed to function as a strict gatekeeper against the passage of large, harmful compounds into the bloodstream. When a person has “leaky gut,” this gatekeeping ability starts to crumble, allowing all sorts of toxins and bacteria into circulation throughout the body. Lowering inflammation by eliminating inflammatory foods is much of the battle. The next step is to repair the damage already done and restore healthy functioning. In functional medicine, we do this by leading patients through the 5R protocol. Each “R” stands for one of the five phases of the protocol. In order, they are: Remove, Replace, Repopulate, Repair, and Rebalance. Our recent blog outlines further details about this 5R program, here. 


Our gut plays a variety of roles that step beyond the usual role of digestion. It is integral to our immune system, our control of inflammation, our mood, our cognition, our stress, even our hormone balance. Any dysfunction in our gut or imbalance of our microbiota effects each of these areas, often causing chronic disease including autoimmune disease. With the help of functional medicine testing, an anti-inflammatory eating style focused on whole foods, and a protocol focused on gut healing, we can help prevent autoimmune flare-ups and improve inflammatory markers. Contact us today for a free phone consultation!

The 5R’s of Gut Healing

The 5R’s of Gut Healing

It is well documented that any dysfunction in the gut can lead to a host of symptoms, including those outside the digestive tract. Gut disturbances can cause fatigue, joint pain, headaches, muscle pain, allergies, autism, ADHD, depression, anxiety, asthma, chronic skin conditions, digestive disorders, and autoimmune diseases. Functional medicine recognizes the interconnectedness of body systems, so when someone comes to us with these symptoms, we often look to the gut first!


The 5R Protocol


There is a functional medicine protocol for gut repair called the “5R’s.” This protocol takes people through the five stages of restoring the balance of the gastrointestinal system, whose function can be compromised through various insults over time. The 5R protocol is used for those with digestive disorders, such as IBS or SIBO. However, the protocol is also used when lab testing reveals dysfunction in the GI tract, even if a person does not have gastrointestinal symptoms. The 5R program stands at the intersection of chronic health issues and poor GI function. 


The 5R protocol has a number of goals:

  • Address dietary and lifestyle issues and to make healthy changes
  • Normalize digestion and absorption
  • Achieve a healthy balance of gut bacteria
  • Encourage a robust detoxification system
  • Promote healing of the gastrointestinal tract


Lastly, the 5R program is not only applicable to those with poor diets. We often find that slim people, athletes, vegetarians, and anyone who is otherwise “healthy,” are just as likely to be good candidates for the program as a person with a poor diet. This is because our gut health is not only determined by our diet, but also by a myriad of other factors, including our physical environment, our early years growing up, our toxin exposures over time, and more. 


Stages of the 5R Protocol


The 5R protocol is so called because it contains five stages of healing that all begin with the letter, “R.” 

1) Remove any element that negatively affects the GI tract. These can be food sensitivities, pathogens, parasites, yeast or bacteria overgrowth. This stage also encompasses decreasing exposure to environmental toxins, food additives, processed foods, etc. The Remove stage involves following some type of Elimination diet where common food allergens are avoided for short-term, while focusing on eating whole-foods. It also involves taking particular supplements and herbs that eradicate overgrowths, parasites, molds, or toxins, where appropriate.


2) Replace the elements that are needed for proper digestion. This includes things like digestive enzymes, hydrochloric acid (stomach acid), bile acid, and proper motility. These are commonly compromised through a variety of factors, such as medications, stress, diseases, aging, and dietary habits. The goal is to replace only what a person needs. This stage is accomplished through taking supplements and practicing meal spacing.


3) Reinoculate the gut with beneficial bacteria. Taking probiotics (as food and as supplements), as well as eating prebiotic foods (which feed healthy gut bacteria), work together to reestablish balanced gut flora, increasing their growth and numbers. This stage involves eating specific foods such as prebiotic foods (artichokes, garlic, onion, leeks, etc), fermented/probiotic foods (tempeh, sauerkraut, miso, cultured yogurt, kefir), and soluble fiber. Probiotic and prebiotic supplements and fiber powder are also available. Be aware that those with SIBO may have exacerbated symptoms when eating these foods (which are largely high FODMAP). They would need to modify this stage or spend longer in the Remove stage.


4) Repair the gut lining now that our immune system no longer has pathogens, toxins, or overgrowths to react to. By now, not only are we free of these harmful agents, but our digestive process if functioning properly and supports a healthy gut flora. Repairing the gut lining involves strengthening the intestinal cells that line our gut. A healthy gut lining allows nutrients to be released into our bloodstream while preventing harmful compounds from doing so. Instead, these compounds must remain in the gut so that they can be eliminated from the body. The Repair stage involves ingesting specific vitamins, minerals, fibers, amino acids, and antioxidants. These all play a role in keeping our gut lining healthy and are often depleted in those who need a 5R program.


5) Rebalance your lifestyle going forward. A healthy gut not only requires healthy food, but also a healthy lifestyle. Proper exercise is critical, not just for our cardiovascular system and emotional wellbeing, but also for our intestinal function. Stress management is another essential aspect relating to gut health. Any stress response (whether psychological or physical) triggers reactionary steps throughout our body, including the slowing of digestive function. Sleep hygiene is our last element of rebalancing. Healthy sleep helps to calm an overactive stress response by regulating cortisol, a stress hormone. 

The 5R Protocol in Practice


Walking through the 5R program takes between three to six months to complete and involves daily commitment to dietary changes; changes which can be fairly demanding and may cause temporary symptoms as your body removes harmful elements. However, not everyone who benefits from the 5R program requires completion of all the stages. Some stages may be bypassed completely or otherwise altered or shortened depending on what specific areas need improvement. For example, a person may already be avoiding harmful elements, such as high-sugar foods or environmental toxins, but they may need a boost in their digestion, like pancreatic enzymes or bile acid. In this case, he would not need to do the first stage, Remove, and can instead begin at the second stage, Replace.


If you struggle with chronic symptoms or disease, it would be worth investigating the underlying cause(s). Do not ignore your gut health or assume that your chronic health issues are unrelated to your gut! It is often said that all diseases begin in the gut. Indeed, the health of our gut affects (and is affected by) most other body systems, from our nervous system (brain) to our immune system. The 5R program is the most comprehensive way to heal the gut, normalize function, and, by extension, improve or reverse upstream chronic disease. Call our team at CustomCare Nutrition to see whether the 5R protocol could help you! Schedule a free phone consultation here

Stress, Anxiety, and IBS

Stress, Anxiety, and IBS

Irritable bowel syndrome (IBS) is a syndrome that causes a collection of symptoms such as abdominal pain, gas, bloating, diarrhea, and constipation. These symptoms range in severity for those affected and can greatly impact a person’s emotional, social, or professional life. In fact, there are strong correlations between emotional and mental health and IBS. Stress and anxiety are often found together in those with IBS. Though it’s not yet clear how they’re related or even which one comes first, they certainly seem to each exacerbate the others. Those with IBS have a more sensitive gut that reacts, not only to certain foods, but also to stress. This makes the effects of stress on those with IBS more severe than those without IBS.


The Gut-Brain Connection

Everything is connected, and this is clearly seen in the human body. Perhaps the connection that seems the most “unconnected” is the link between our emotional centers of the brain and the functioning of our gut. This is called the gut-brain connection (or gut-brain axis), and describes the nerve-signaling between the central nervous system (including our brain) and the enteric nervous system (which is found in our gut). This “gut” nervous system is composed of 100 million nerve cells that line our digestive tract, from esophagus to rectum. It controls things such as swallowing, digesting, releasing enzymes, and communicating back and forth with our central nervous system (which includes our brain). In this way, our gut has the power to influence our brain’s reaction to stimuli. This connection becomes more pronounced and has heightened responses during moments of stress. When our brain experiences stress, so does our gut.


IBS and Anxiety

For those with IBS, irritation to the gastrointestinal tract launches a stress response which signals the central nervous system to trigger large emotional shifts, such as anxiety and depression. These emotional shifts tend to be stronger in those with IBS due to their heightened stress response. The prevalence of anxiety in those with IBS is quite strong. Around 60% of people with IBS develop anxiety or depression, with generalized anxiety disorder as the most common mental disorder in that population. 


Types of Stress

Not only is mental health more affected in those with IBS but the stress response is also heightened. Stress is any event (perceived or actual) that disrupts the balance between our mind and body. Stress can be acute or chronic and includes daily inconveniences, life-threatening trauma, and everything in between. Lastly, stress can be physical or psychological in nature. Physical stress includes things such as surgery, infection, and working out, while psychological stress is what we’re more accustomed to and includes emotional reactions, relationship problems, job loss, financial struggles, etc. 


IBS and Stress

In someone with IBS, stress of any kind can exacerbate IBS symptoms. Depending on which type of IBS a person has, their stress response can trigger abdominal pain, diarrhea, or constipation. Gut motility, for example, is affected to a greater extent during a stress response in those with IBS than it is for those without IBS. Motility in this context means the movement of the large intestine that causes rhythmic contractions to push digested food through our digestive tract. 

In response to stress, those with IBS can experience either a speeding up or a slowing down of gut motility. Having faster motility leads to diarrhea while slower motility leads to slow gastric emptying and constipation. 

Another item about impaired motility is that it can affect the natural balance of our gut bacteria and actually cause an overgrowth. This overgrowth is what characterizes SIBO (small intestine bacterial overgrowth) and is why those with IBS often develop SIBO or are greatly helped by following a low FODMAP diet. Interestingly enough, chronic stress alone is enough to set our gut bacteria off-balance and cause dysbiosis (even without the help of slowed motility).


Ways to Cope

With all the communication that takes place between our gut and our brain, it’s important to make sure that only healthy messages are being sent. By this I mean that a healthy brain translates to a healthy gut (this goes for anyone with a gut and a brain, not just those with IBS!!). The good news is research shows that stress management can help prevent IBS symptoms (or ease any flare-ups). The following tips can help you formulate a stress management plan to get your brain and your gut on the same wavelength. 

Cognitive Behavioral Therapy (CBT) is a mind-body therapy that helps alter the way we think and respond to stress. It provides new perspectives while helping us regain control and confidence with effective coping strategies.

Keep a symptom journal. Document your symptoms on a daily basis to help you make connections between which thought processes or events may be triggering your IBS symptoms. Once you understand your specific stressors, take steps to spot them coming and avoid them.

Mindful eating. Help soothe your gut by practicing mindfulness during mealtimes. Create a peaceful eating environment where you can sit away from daily distractions. Focus on how your meal will nourish you and eat slowly, chewing thoroughly. 

Gratitude. Take control over your stress or anxiety by practicing daily gratitudes. Focus on what you’re grateful for each day while letting go of any negative thoughts, to-do lists, worries, or busy schedules. Many people opt for a gratitude journal to remind themselves of past thoughts of thankfulness.

Relax. Relaxation will look different for everyone. Sometimes it’s a hobby, sometimes it’s taking a walk, listening to music, or maybe even the act of washing dishes. The important thing is to set aside time to do what you enjoy. This activity should also be relaxing for you. Aim to relax in this way at least twice a week and notice how your attitude, emotions, and overall well being brightens up. 

Daily movement. Those with IBS would do best with gentle activities that don’t trigger symptoms. Such movements support the gut-brain connection while lowering stress. Walking, yoga, bike riding, and swimming are all great options. 

Acupuncture. Many people with IBS report that acupuncture helps minimize stress and anxiety. In fact, acupuncture can be effective in a variety of gastrointestinal disorders and symptoms from nausea to ulcers, Crohn’s disease to IBS. Importantly, acupuncture can also help relax an overstimulated fight or flight response (stress response).


Those with IBS usually have several triggers that bring on symptoms. Not all of them are food related though. Stress and anxiety are strongly related to IBS and can affect IBS symptoms. The communication channel between our gut and our brain is what allows our gut health to affect our brain health (and the other way around). Lowering stress and anxiety triggers will go a long way towards alleviating or even preventing IBS symptoms. Call our team at CustomCare Nutrition for a free phone consultation to get started on a gut healing plan for your IBS.

Fiber and the Microbiome

Fiber and the Microbiome

Fiber is much more than a way to keep you regular. It has several benefits for our health including weight loss, blood sugar control, and lowered risk for chronic disease. It is also the key to maintaining the health of our gut bacteria. However, with all these benefits, most of the world does not get enough fiber. The WHO (World Health Organization) recommends, on average, about 30 grams of fiber daily, however, Americans eat between 10-15 grams of fiber per day. This is not quite surprising when we consider that fiber only comes from plant foods, something Americans (and other Westernized countries) usually consider as an afterthought or a chore.

Let’s dive into the types of fiber and the role they play in our health, specifically our microbiome. We’ll also discuss how to keep our gut bacteria well fed and the importance of eating a variety of high-fiber foods.


Types of Fiber

At its core, fiber is a type of carbohydrate that cannot be digested by our body. In fact, we don’t have the enzymes necessary to break them down, so they pass through our digestive system unchanged. Fiber comes by many names, each describing their unique biochemical structure. Names such as cellulose, pectins, oligosaccharides, dextrins, beta-glucan, polydextrose, galactan, inulin, and more.

Despite these various names, fiber comes in two main types: soluble and insoluble. It is best to eat a mix of both types unless instructed otherwise by a functional medicine physician. Those who are having a flare-up of IBD (Inflammatory Bowel Disease), or who are in treatment for SIBO (Small Intestine Bacterial Overgrowth), have diverticulitis, or have chronic diarrhea, are candidates for limiting certain types of fiber. 

Soluble fiber dissolves in water and is fermentable. It forms a gel-like substance in our gut and slows down bowel transit time (the time it takes for food to pass through our system). This allows soft, well-formed stools. 

Insoluble fiber does not dissolve in water, remaining intact throughout our digestive system. It is the main bulking agent, speeding up our bowel transit time and helping with constipation. Most insoluble fiber is not fermentable. 

Most plant foods contain both soluble and insoluble fiber.


Food For Gut Bacteria

Feeding our gut bacteria perpetuates the growth and variety of bacterial species while playing crucial roles in our health. Beneficial gut bacteria help with weight control, blood sugar balance, cognitive function, immune function, inflammation, digestive disorders, and more. There are three sources of food that our gut bacteria uses to function properly.

Fermentable Fiber

You may have noticed the mention of fermentation when describing the types of fiber, above. When a food is fermentable (like soluble fiber and some types of insoluble fiber), it means our gut bacteria literally ferment it (or digest it) once it reaches our large intestine. Fermenting these fibers is how our microbiome gets its fuel for energy. Fiber serves as their food source. 

Resistant Starch

Another food source for our gut flora is resistant starch. Starches are the main type of carbohydrates in our food and some of them resist being digested. Much like fiber, these resistant starches pass through our digestive tract unchanged. Although not a type of fiber, resistant starches are fermentable just like soluble fiber. This makes it another food source for our gut bacteria. 


Similar to fermentable fiber and resistant starches, prebiotics are also carbohydrates that are non-digestible by our bodies, making them a great food source for our gut bacteria. Most prebiotics are found in plant foods and are considered a type of soluble fiber. However, other prebiotics come from non-fiber sources such as lactulose (made from lactose) and polyunsaturated fatty acids (such as that found in fatty fish).

The main difference between prebiotics and other non-digestible carbs is that prebiotics are selectively used by our microbiota. We have more than 500 species of bacteria living symbiotically in our gut; ideally containing more helpful bacteria than harmful. Unlike fermentable fiber and resistant starches, not all bacterial species are able to digest prebiotics. Rather, prebiotics are digested by certain beneficial bacteria such as those seen in probiotic supplements (Lactobacillus and Bifidobacterium). 

A Note About SIBO

Fermentable fibers, resistant starches, and prebiotics should be limited or avoided short-term by those who have SIBO or who have IBS symptoms. Feeding gut bacteria is only a good thing when the bacteria are where they’re supposed to be, in the large intestine. However, if they become overgrown elsewhere (as in SIBO), then eating these foods will feed and perpetuate the overgrowth and cause symptoms.


Short-Chain Fatty Acids

When our gut bacteria digest (ferment) fiber and resistant starches, they produce short-chain fatty acids (SCFA) inside our large intestine. The most beneficial (and most studied) SCFA is called butyrate, which can also be taken in supplement form. These fatty acids benefit our gut as well as our immune system. 

In our gut, SCFA’s are responsible for feeding the cells that line our large intestine, and maintaining the health of our intestinal barrier. In this way, SCFA’s protect our gut health and reduce gut inflammation. This leads to improvements in digestive disorders such as SIBO, IBS, ulcerative colitis, and Crohn’s disease. Furthermore, butyrate is thought to interrupt the growth of colon cancer cells and reduce the risk of this cancer.

Butyrate, more than other SCFA’s, has anti-inflammatory effects throughout the body (not just in the gut). They even play a role in the specialization of immune cells. Lowering inflammation and strengthening the immune system are key ways in protecting ourselves against chronic disease and acute infections. 


Benefits of Fiber

Increasing fiber in your diet has additional health benefits beyond those that come from butyrate and other short-chain fatty acids. Fiber can improve glucose balance, lower body weight, and reduce cholesterol levels, all of which are protective against diabetes and cardiovascular diseases. Various types of fiber can increase the feeling of fullness (satiety), reduce hunger, regulate the frequency and consistency of stool, and improve mineral absorption in the gut, particularly calcium and magnesium.   


Diversify Your Fiber Portfolio

It’s important to get your fiber from a variety of sources rather than sticking with just one or two high-fiber foods. This is because fiber foods each contain different types of fiber with different combinations of carbohydrates and starches (such as beta-glucan, inulin, or dextrin). Each type of fiber imparts unique benefits and enables our gut bacteria to thrive and maintain diverse bacterial species. 

Keep in mind that seemingly simple events in our lives, such as illness, poor diet, stress, environmental toxins, or antibiotic medication, all have a negative effect on our gut bacteria. Specifically, these insults greatly decrease the diversity of species. A person with low diversity of gut bacteria is a person at high risk for chronic disease, digestive disorders, infections, and a weakened immune system. 


A diversity of high-fiber foods creates a diversity of healthy gut flora 


High-fiber foods are found chiefly in legumes (beans), whole grains (quinoa, oats, wheat, etc), and starches (like potatoes and brown rice). They are also found in good amounts in various vegetables, fruits, and nuts/seeds. If we’re only talking about fermentable fiber, which is the food source for our gut bacteria, beans contain the highest amount. In fact, a one-cup serving of beans contains roughly half (15 grams or so) of the recommended intake of daily fiber!

Be sure to include whole grains and starches along with your vegetables and fruit in order to increase fullness and carry you to the next meal. Also, be aware that eating too much fiber, too fast, can lead to excessive gas, bloating, or abdominal discomfort. This is commonly the case with foods high in fermentable fiber or soluble fiber, especially if you aren’t used to eating a high-fiber diet. If you get digestive symptoms after eating canned beans, be sure to rinse them in a colander until all the bubbles are gone. 


Fiber is an essential part of our daily diet even though it is often overlooked. Most people do not get enough fiber as we continue to gravitate towards highly processed foods that are stripped of fiber (and other nutrients). Not only does fiber keep us regular but it is the main food source for our gut bacteria. Keeping these bacteria well fed is key to maintaining the health and function of beneficial species while harmful species are kept at bay. Not only that, but when our gut bacteria digest fiber, they produce short-chain fatty acids that play key roles in the integrity of our gut lining as well as in reducing inflammation and influencing our immune system. Fiber imparts other benefits including blood sugar control, weight loss, mineral absorption, and protective against chronic disease. Eating a variety of plant foods high in fiber will ensure the health and diversity of our gut bacteria.