By Sheila Dobson, BA NC

This is part one of a three part series on digestive system health and healing.

Gut Health is Critical For Overall Health

All illness — virtually — begins in the gut. Hippocrates is said to have made this statement over 2 thousand years ago. This means that anyone seeking to improve a health condition would be wise to pay close attention to their intestinal and digestive health.

Despite the critical role of intestinal health in overall health, many practitioners today still pay only superficial attention to this important principle of health.

Recent Research On Intestinal Health

Recent research has been confirming what Hippocrates knew. Hippocrates didn’t do double blind studies…but he observed that intestinal problems always seemed to be at the root of other health problems.

In the modern world we have the luxury of knowing much detail about how aspects of our digestive process fit with our other bodily processes. Scientific and medical research has produced important knowledge that can guide us in health recovery. Let’s look at just two examples of what recent research has shown.

Good Bile Acid Production is Critical For Good Gut Health AND The Health Of The Whole Body

Research performed mostly in the past ten years shows that there is a critical role played by bile acid production on both intestinal health and the health of the body as a whole – for example processes like energy production and blood sugar regulation do not proceed correctly without good bile production and bile flow.

Quick review here for those who may be foggy on bile. Bile is the substance produced by the liver and stored in the gallbladder that helps with fat digestion and digestion and detoxification generally.

Bile is made from cholesterol. Bile acids are the main type of compound found in bile. These acids are detergent-like molecules that help us digest fats.

Bile enters the small intestine from the gallbladder whenever we eat anything containing fat. It is extremely important for the absorption of fat soluble vitamins such as vitamin A, D, E and some forms of vitamin K.

For decades experts would have told us that this is the main if not virtually the only function of bile – to help us digest fats. However, what is now understood is that without good bile acid production, much, much more than just fat digestion suffers. Bile has many other roles to play both in and outside the intestines besides just helping us absorb fats.

We now know that the “epithelium,” which is the type of tissue that lines our intestines, is dependent for its maintenance on an adequate flow of bile acids. So, essentially, poor bile production leads to poor health of the intestinal lining.

In and of itself, this is an interesting discovery, and it is a pretty big deal. If the cells lining your digestive tract are not in good health, then there will be many consequences downstream from this point, obviously. But this is only the beginning. There are MANY other processes in which bile acids play a role — here’s a partial list:

• the regulation of nutrient absorption
• cellular growth and repair
• energy metabolism
• the regulation of glucose and lipid (fat) metabolism
• the modulation of the gut microbiome, and even
• the secretion of intestinal hormones such as the now well known GLP-1 hormone (Lin, 2025)

Let’s take a closer look at two of these processes that bile flow is needed for.

The first, regulation of nutrient absorption, is fairly self explanatory. This means, basically that our bodies have control to a degree over how much of any given nutrient we absorb. So, fortunately, even if we eat a whole bucket full of oysters, we probably won’t absorb ALL the zinc and copper they contain, unless of course, all of it is actually needed! Our bodies are quite amazing and intelligent.

Of course, the process works in reverse too; if a nutrient is scarce in the diet, the body can “up-regulate” absorption. So, for example, if someone has a vegetarian diet, which is relatively low in absorb-able iron, the body can “up-regulate” iron absorption to compensate.

Clearly, the regulation of nutrient absorption is a very important digestive function that helps maintain good health! The fact that our bodies can regulate nutrient absorption makes it possible to be well-nourished on a large variety of different types of diets, even some diets that are much less than optimal in terms of nutrient content. Good bile flow is needed for this process to function correctly, but poor bile production would mean the regulation system won’t work like it is meant to. The result will be in virtually all cases, lower nutritional status.

Lower nutritional status. Is this really a big deal? Well, yes, in my opinion it is. It is already difficult to be properly nourished in the modern world with our nutritionally depleted food supply, but when our body’s regulation of nutrient absorption becomes impaired, it just adds another layer of difficulty to being properly nourished.

Now let’s look at another item from the list: “Energy metabolism.” Energy metabolism means the process by which the body turns food into energy. You may recall from a biology class that every cell in the body makes energy and uses energy to conduct its cellular processes.

Bile plays a role in regulating this process. It activates a certain receptor in our cells called TGR5. When the TGR5 receptor is activated, it triggers other cellular messenger molecules that then cause cellular processes to proceed. A crude analogy would be to compare TGR5 to the spark that is needed to make your car’s engine function properly. While gasoline is the fuel (kind of like food in the human body), the fuel can’t be burned efficiently or do work — can’t make the car go — without the spark. The analogy is not perfect but the point is that the TGR5 receptor must be stimulated by bile for cells to receive the signal that causes them to make energy and perform other functions.

As you might suspect, for this reason, poor bile production can result in, you guessed it — poor energy production — leading to — you guessed it — obesity (Zangerolamo et al, 2025).

Of course, obesity is only one possible result; there are many other problems that can develop as a result of poor bile production. Some people might be more prone to develop obesity when fuel is not burned efficiently and cells are not stimulated properly to produce energy, but others might develop other types of problems, perhaps constipation, or gallstones, or metabolic syndrome.

The above examples are only two of the ways in which bile acids are needed to maintain overall health.

As you can see there are a number of processes that occur in our bodies that require proper signaling to proceed correctly. The signals are contained in bile. If we want to be healthy, we need to take care that our liver and our bile flow are functioning correctly.

The Microbiome and Its Effects on Human Health

Now let’s look at a different example of how intestinal health impacts overall health.

There is a huge area of study that has exploded in recent years which looks at the human microbiome.

“Microbiome” is just a fancy word for the microbial community within the intestines and elsewhere in the body. We have trillions of microbes that inhabit our bodies, inside and outside of it. In fact, we have more microbial “bodies” inhabiting us, than we have cells in our body.

“The human microbiome is composed of communities of bacteria (and viruses and fungi) that have a greater complexity than the human genome itself.”

amon, p., sanderson, I. 2017

In recent years it has become clear that a healthy microbiome is needed for a vast array of functions inside the body. These include protection against pathogens, synthesis of vitamins, immune system function and development, intestinal blood vessel development (needed for nutrient absorption), promotion of fat storage, short chain fatty acid production (needed for the health of the intestinal lining), and modulation of the central nervous system (including production of many neurotransmitters). This is not just a collection of microbes that happen to live in our gut and give us a few benefits in exchange for us providing them a home. They are the basis of our health!

Let’s look at what the research shows happens when the immune system and other bodily processes lose control over the composition of the microbiome.

Dysbiosis and SIBO – Causes of Chronic Disease

SIBO and dysbiosis are intestinal health disorders that are similar but not exactly the same. Dysbiosis simply means a less than healthy mixture of microbes in the intestinal environment — this could be an overgrowth of pathogenic species or simply a lack of certain beneficial species, or a lack of diversity or some combination of these.

SIBO is a bit more severe and is a type of dysbiosis. SIBO means small intestinal bacterial overgrowth.

Normally most of the “microbiome” resides in the large intestine. When a person has SIBO, bacteria from the large intestine have migrated into the small intestine where they don’t belong. They may be overpopulating this critical digestive organ and interfering with its functions. There may be pathogenic species invading the small intestine of course, also.

Dysbiosis is extremely common today. In fact, well known experts such as William Davis, MD, author of the books, Wheat Belly and Super Gut tell us that some degree of dysbiosis is the norm now, not the exception. Dr. Davis makes the connection of dysbiosis to all the major categories of disease that are so prevalent today. He discusses SIBO at length as well, and recommends strategies for correcting both conditions.

Now let’s look at what the research shows about how these conditions connect with chronic disease.

SIBO has been linked in recent research to twelve different categories of disease (Roszkowska, 2024). Not twelve diseases, mind you, but twelve CATEGORIES of disease.

These twelve categories include:

• gastrointestinal disorders
• autoimmune diseases
• cardiovascular disease
• metabolic disease (such as diabetes, some forms of obesity, mitochondrial disease and others)
• endocrine disorders
• nephrological (kidney) disorders
• dermatologic diseases
• neurological disorders
• developmental disorders
• mental disorders
• genetic diseases
• gastrointestinal cancers

You might be wondering, are there any other categories of disease? Seems like the list covers a huge proportion of human ailments.

Basically, what this is showing us is that, if you have SIBO, it appears you will almost certainly, eventually develop more systemic health problems.

Logic might be suggesting to you that perhaps the reverse is true as well. In other words, if you have a health condition that lands in any of the categories listed above, maybe there is a connection — in fact maybe the ultimate cause — is associated with the health of your gut?

I suspect if we were able to ask Hippocrates what he thinks about all this, he’d say “That’s right. I told you more than 2,000 years ago, all disease originates in the gut.”

Why Intestinal Dysbiosis Affects The Whole Body

If a person has either dysbiosis or SIBO (think of SIBO as simply a particular form of dysbiosis), essentially we are dealing with a disordered microbiome, and more than likely, pathogens present at levels that cause harm as well as a lack of adequate diversity and perhaps the lack of certain species that are needed for optimal health.

The pathogenic species produce problems (whether directly or indirectly) like ulceration or inflammation; quite often both of these.

Pathogens also increase oxidative stress and overburden the liver and immune system. Not only that, they produce byproducts that can affect thyroid function, brain function and many other processes. So, this is a lot of damage from a little disordering (or a lot) of the microbiome!

Ulceration and inflammation naturally will interfere with the small intestine’s ability to function in its very important roles of digestion and absorption. This is likely to lead to nutritional deficiencies because the small intestine is where most of the digestion and absorption of nutrients occurs. Disturbances of this process can have potentially serious consequences. Not only that ulceration, inflammation and the presence of pathogens further drain the body’s energy reserves and nutritional resources.

The lack of certain beneficial species is an issue beginning to be more and more fully understood. Here are just a few examples of why diversity and the presence of key strains of bacteria are so important.

A newly identified species called Akkermansia muciniphila is now known to assist the body to maintain a proper mucous layer and proper barrier function, as well as producing metabolites that have other beneficial effects.

Other species too, have particular roles which are essential for good health that are not necessarily filled by just any bacteria; in other words, the right species need to be present or potentially a particular function is not carried out. For example, certain species produce butyrate (butyric acid) which is a fuel source for the cells that line the colon. Others produce serotonin, among them, Limosilactobacillus mucosae. Serotonin is needed for proper gut motility and for stable mood and mental function (Moretti, C et al., 2025).

Truly, volumes could be (and have been) written about all the functions of the various microbes within our microbiomes. A single, healthy human microbiome has, typically 300-some different species of bacteria. There are some 1,000 or more different strains of bacteria that can be found in the human microbiome.

Because of the critical functions carried out by our micobiomes, in particular the intestinal microbiome, it is a bad deal all around when the microbiome of a person is very compromised. This comprising can have to do with excessive levels of pathogens, or the loss of entire groups that are normal inhabitants of a healthy gut, and other problems.

Trying to overcome health concerns without addressing the role of digestion and intestinal health — particularly the adequate production and secretion of bile and the health of the microbiome — is a bit like trying to row your boat to the shore with a broken paddle and a hole in the bottom of your boat; a lot of effort will be wasted and you still won’t get where you want to go.

Conditions like acne, brain fog, irritability, indigestion, reflux or GERD, constipation, food allergy, autoimmunity, anxiety, depression, poor immune function, even obesity and many other conditions all connect to the health of the intestines and in particular to the health and diversity of the microbiome.

Sheila Dobson, NC

Please also read:

References:

Zangerlamo, L. et al., The critical role of the bile acid receptor TGR5 in energy homeostasis: insights into physiology and therapeutic potential. Int. J. Mol. Sci. 2025. 26, 6547

Amon, P, Sanderson I., What is the microbiome? Arch Dis Child Educ Pract Ed. 2017; 102:258-261.

Davis, W. Super Gut; Balance, 2022.

Moretti, C., et al., Identification of human gut bacteria that produce bioactive serotonin and promote colonic innervation. Cell Reports 44, 116434, October 28, 2025

Duboc, H., et al., The bile acid TGR5 membrane receptor: from basic research to clinical application. Digestive and Liver Disease 46, 2014; 302-312

Secretion of Bile and the Role of Bile Acids In Digestion. Colostate.edu. https://vivo.colostate.edu/hbooks/pathphys/digestion/liver/bile.html (accessed 2026-07-16).