Category Archives: Gastrointestinal Health

You Are What You and the 100 Trillion Bacteria in Your Gut Eat

iStock_000014496302SmallWe have all heard the saying you are what you eat. While there is a lot of truth to that statement, it is becoming clear that it may need to be updated to “you are what you and your gut bacteria eat.” Research into the function of the 100 trillion bacteria that call our gastrointestinal tract home has been exploding over the past few years. We now know that they are not merely uninvited “house guests” but instead play active roles in our health as well as metabolic activity effecting our digestion, immune function, hormonal function and mood.


One area of research that has received much attention is the discovery that gut bacteria have an effect on the development of obesity, metabolic syndrome and type 2 diabetes. People with higher levels of bacteria in the Firmicutes family and lower levels of bacteria in the Bacteroidetes family seem to be more likely to be obese and are at an increased risk of developing diabetes and metabolic syndrome. The increased risk of diabetes and metabolic syndrome appears to not just be a result of the obesity, but instead is related to effects on inflammation and liver function. The increased weight gain is in part due to the fact that some bacteria in the Firmicutes family are very good at digesting starches and fibers that you can’t digest and converting them in to short chain fatty acids that the body can then use as energy. This ads to the net energy intake on a day to day basis and so you may be getting more “calories” out of your food than you think. The bacteria that do this are not pathogenic or “bad” bacteria. In fact some of them are strains of Lactobacillus bacteria usually thought of as being health promoting.


A study published in Biology Letters in January found that people living in northern climates, such as Maine, have higher levels of Firmicutes bacteria and lower levels of Bacteroidetes bacteria and that this correlates with the rates of obesity in the regions studied. From an evolutionary standpoint there is a benefit to this as an increase in energy production would increase the likelihood of survival through the cold harsh winter. Why this shift occurs is not known at this time. It may be that there is an environmental input such as temperature or amount of daylight that stimulates the growth of Firmicutes bacteria. It is known that dietary factors can have a large effect on the balance of Fimicutes and Bacteroidetes bacteria. A diet higher in fat and refined sugars will increase Firmicutes levels while a diet lower in fat and higher in plant polysaccharides (found in fruits, vegetables, legumes, and whole grains), will increase the levels of Bacteroidetes bacteria. In general there does tend to be an increase in fat and sugar intake during winter and a decrease in fresh vegetable intake the further away from summer that we get.


A big pharma approach to this (and I’m sure some drug company is working on this) would be to design an antibiotic that kills only the Firmicutes bacteria and spares that Bacteroidetes bacteria. While this could have short term benefits, in the long term many of the Fimicutes bacteria have benefits and getting rid of them could lead to increases in allergies, depression, and inflammatory bowel disease to name but a few.


A better approach would be to eat a diet lower in saturated fat and sugar and eat more plant foods. In addition,a study published in the journal Chemico-Biological Interactions showed that a high intake of poly-phenols found in green tea, apples, and cider or wine vinegar preferentially increase the levels of Bacteroidetes bacteria. While Lactobacillus bacteria can have many benefits, it may also not make sense to supplement with them when levels are already high. Focusing on probiotics higher in Bifidobacteria (a member of the Bacteroidetes family) along with prebiotics and colonic foods that increase their levels may be more beneficial and less likely to negatively impact the Fimicutes/ Bacteroidetes balance.


You can find out what your ratio of Firmicutes to Bacteroidetes bacteria is by doing stool test that looks not only at this ratio but also uses DNA markers to determine the levels of various bacteria in your gastrointestinal tract. Having this information can help in determining dietary changes that will be helpful along with determining if probiotics are necessary and if so what type. If you are interested in finding out more about this test, or if you would like to have the test done, you can call my office at (207) 805-1129 or email me at [email protected]

The Road to Health is Paved with Good Intestines #6: The Large Intestine and Its Microbial Inhabitants.

iStock_000012048107Small-300x300In my last blog post, we made our way through the 22 feet of the small intestine. Once what has remained of our food completes that journey, it goes through a gate called the illeocecal valve and finds its way into the large intestine. The large intestine is only about 5 feet long but the diameter of the tube is quite a bit larger than that of the small intestine, thus its name.

By the time the food remains make it to the large intestine, our own digestion of it has completed. This does not mean that digestion is over though. The 5 pounds of bacteria that inhabit the large intestine are happy to feed upon whatever is left. They ferment carbohydrates that you were not able to digest and in doing so produce b-vitamins such as biotin, vitamin K, and short chain fatty acids that serve as an energy source not only for the cells of the intestine but for the rest of the body as well. Short chain fatty acids also help with the repair of cells in the large intestine and provide defense against colon cancer and inflammation in the large intestine. Read more »

The Road to Health is Paved with Good Intestines #5: The Small Intestine

iStock_000012048107Small-300x300When we last left the gastrointestinal tract we were in the stomach where stomach acid and enzymes in conjunction with the mechanical forces of the stomach’s muscles were breaking down our food into a liquid known as chyme. When the gate at the bottom of the stomach called the pyloric sphincter opens, the chyme leaves the stomach and begins travelling into the small intestine.

Despite its name, the small intestine is the longest part of the gastrointestinal tract with the average length of 22 feet. If this wasn’t big enough, if you were to pull it completely taught, the surface area would be the size of a tennis court. This is because the inner surface is shaped into a multitude of finger like projections called villi. When you look at it under a microscope it resembles the Down East coast of Maine. This giant surface area increases the nutrient absorption ability of the small intestine.

Before digestion and absorption can be completed more digestive enzymes and other chemicals are needed to continue breaking things down. Some of these enzymes are released directly by the cells of the lining of the small intestine. Others are released through a small connecting tube by the pancreas. Bile, released by the liver and stored in the gallbladder is squirted in to emulsify fats in a similar way to how dish detergent works to clean grease off of pans. Once the chyme is mixed is mixed with these enzymes and chemicals the carbohydrates, fats, proteins, vitamins, and minerals are then absorbed across the lining into the blood stream.

In addition to its functions of digestion and absorption, the small intestine houses 70% of your immune system and helps to distinguish between molecules you can absorb and friendly bacteria from non-digestible food particles and pathogenic organisms. More of your immune system is located in your gut than any organ in your body because it comes into contact with more foreign molecules and organisms than any other organ and the lining of the small intestine is only one cell thick.

When your gut immune system is working well it is able to handle the load that it is exposed to on a daily basis. However, a number of factors can cause it to become overwhelmed such as:

  • Eating food high in sugar and unhealthy fats
  • Eating a diet low in fiber
  • Incomplete digestion caused by low stomach acid or impaired digestive enzyme function.
  • Exposure to food allergens or environmental toxins
  • Excessive or chronic stress
  • Nutrient deficiencies
  • Viral, bacterial, or fungal infections.
  • Imbalances or overgrowth of normal gut microbes.

When the gut immune system becomes overwhelmed the single cell lining of the small intestine can become damaged leading to a leak in the barrier. This can allow semi digested food particles and bacterial toxins to cross the barrier leading to food allergies and inflammation. More and more evidence is linking inflammation and altered immune response in the gastrointestinal tract with chronic illnesses ranging from rheumatoid arthritis to heart disease to certain forms of cancer.

Luckily there are simple steps that you can take to help support a health small intestine and the gut immune system.

  • Eat a diet that contains optimal levels of nutrients to support the gut immune system including: vitamin A (green leafy vegetables, yellow and orange vegetables, fruits, egg yolks, and oily fish such as sardine), vitamin C (citrus fruit, blackberries, raspberries, kiwis, cruciferous vegetables, and sweet potatoes), zinc (pumpkin seeds, whole grains, and legumes), and fiber (fruits, vegetables, legumes, whole grains, nuts, and seeds).
  • Consume foods high in glutamine. Glutamine is an amino acid that is used by the cells of the small intestine for fuel. Good food sources include: cabbage, spinach, fish, chicken, eggs, legumes, nuts, seeds, and parsley.
  • Eat healthy fats. Healthy fats can help to support proper immune function and reduce inflammation. Good food sources of fats include wild cold water fish (sardines, salmon, and anchovies), avocados, olive oil, walnuts, almonds, coconut oil, pumpkin seeds, flax oil, and flax seeds.
  • Maintain optimal levels of stomach acid. As mentioned in the last blog, stomach acid helps to destroy harmful bacteria, parasites, and viruses. By getting rid of them before they get to the small intestine it decreases the load that the gut immune system has to deal with.
  • Avoid food allergens and food sensitivities. Eating foods that you are allergic to or that you are sensitive to can over activate your gut immune system leading to further damage and inflammation. An allergy elimination diet can be helpful in identifying foods you are reacting to.
  • Reduce stress. Stress increases your inflammatory response and has a negative impact on the gut-immune system. Exercise, meditation, yoga, journaling, massage, and breathing exercises can all help reduce the stress response.

Anything that was not absorbed in the small intestine will continue its way down the gastrointestinal tract where it will serve as food for our gut bacteria and ultimately be excreted. In the next blog we will finish our journey through the gastrointestinal tract as we make our way through the large intestine and meet the trillions of bacteria that call it home.

The Road to Health is Paved with Good Intestines #4: The Stomach

iStock_000012048107Small-300x300Last month our journey through the gastrointestinal tract took us from the mouth down the tube called the esophagus.  As the journey continues in this the fourth blog in this series, we have come out of the esophagus and found our way into the stomach.

When most people think about digestion, the stomach is probably the first thing that comes to mind.  The stomach is a muscular, elastic pear shaped bag that can comfortably hold about a quart of food.  It is in the stomach where the real physical dis-assembly of the food you ate takes place.

The stomach has three tools that it uses to accomplish this.  First it produces hydrochloric acid that breaks down the proteins in our food and kills bacteria that may have been growing on our food to prevent infection.  Second it produces digestive enzymes that further help to rip apart proteins, fats, and carbohydrates.  Third the muscular mechanical action of the stomach physically macerates the food into small particles allowing the acid and the enzymes to work even more effectively.

From the time that you eat a food, it typically takes 2 to 4 hours for the stomach to work on breaking it down before letting it continue on to the small intestine.  By the time it is released into the small intestine it should bear no resemblance to the meal that you ate.

Unfortunately, there are many things that can impair this function from occurring optimally such as:

  • Eating while you are under stress or eating without paying attention to what you are eating.
  • Eating too fast and not chewing your food well.
  • Taking antacid and acid blocking medications
  • Eating too much
  • Low stomach acid production
  • Infection with the bacteria H. pylori

Some of the consequences of impaired stomach digestive function include:

  • Stomach pain
  • Reflux or heartburn
  • Gas and bloating
  • Nausea
  • Constipation or diarrhea
  • Nutrient deficiencies or insufficiencies
  • Increased risk of developing food sensitivities
  • Increase risk of developing chronic bacterial infections of the small intestine.

The stomach actually works better when it is not completely full.  Have you ever tried to use your blender when it is too full? You end up with a big mess all over the kitchen and your smoothie doesn’t get blended very well.  If the stomach is too full it can’t break things down very well.  In addition pressure builds up and the stomach contents can find their way back up into the esophagus.  When this happens it can cause the burning that we associate with heartburn.

In order to optimize he ability of your stomach to adequately break down you food and prepare it for its journey through the small intestine, I recommend the following:

  • Try to eat in a calm, relaxed, mindful state.  (See the first blog in this series for more details.)
  • Chew your food thoroughly before swallowing.  (See the second blog in this series for more details).
  • Do not over eat.  Eat only until you are about 80% full to allow your stomach room to do its work.
  • Eat slowly to allow the stomach time produce stomach acid and enzymes.
  • Avoid long term use of antacids or stomach blocking medications.  If you have to take these daily, it is time to seek professional guidance to determine and fix the underlying issues.
  • To help further stimulate the digestive function consider taking digestive bitters (see last month’s blog) or drink the juice of half a lemon in 3 to 4oz of room temperature water before you eat.

If symptoms persist, you may need to supplement with digestive enzymes or hydrochloric acid.  Working with a practitioner who is knowledgeable about optimizing digestive function can be helpful in determining if these therapies may be helpful and how best to use them.

You may be wondering why the hydrochloric acid in your stomach doesn’t it just burn a hole right through it.  Fortunately for us, the lining of our stomach is protected by a layer of mucous.  However if that mucous layer breaks down it will allow the acid to burn a hole in the lining.  This is what happens when someone develops an ulcer.

While it used to be though that most ulcers were caused by stress, it has since been found that there is a bacteria called Helicobacter pylori that is to blame.  While most bacteria are killed off in the acid environment, H. pylori can thrive in it leading to irritation, inflammation, and ulceration of the stomach lining.  When this happens, it not only hurts, but it also impairs digestion by decreasing stomach acid production and it impairs absorption of certain vitamins and minerals such as zinc and vitamin B21.

While treatment of stomach ulcers can often require the use of antibiotics, the licorice compound that I mentioned in last month’s blog (DGL) can often be helpful in restoring the mucous lining to the stomach and getting rid of the bacteria H. pylori. 1 to 2 tablets chewed before each meal can often helped to relieve symptoms and allow healing to take place.

Severe cases of ulceration can lead to blood loss and be a serious health concern.  If symptoms persist or get worse, seek care from your health care practitioner.

Now that our food has been effectively broken down by the stomach, in our next blog we will look at how we absorb those nutrients in the small intestine and what can cause that ability to be impaired.

The Road to Health is Paved with Good Intestines #2: The Mouth

mouth-open-huge307x379-243x300Summer is a time of many get togethers and with that comes a lot of opportunities for eating.  As we continue our exploration of the digestive tract, now that you are in the right mind state for optimal digestion it’s finally time to take a bite.  (If you missed the first blog in this series, it can be found here.)

Chewing is the first in many steps towards breaking down your food into small particles that your body can absorb and utilize for energy, and all of your nutritional needs.  Chewing is also the only one of these breakdown mechanisms that we completely control. Our teeth are designed to tear off bites of our food and then mash it down into a paste.  In addition to the teeth grinding our food up, chewing also allows the food to be mixed with saliva and digestive enzymes that help to chemically break down the food.

Ideally by the time the food hits the stomach it is already well on its way to being broken down.  On a basic level, if you are not chewing, the food particles are too big to be properly digested.  It is going to be more difficult for it to make its way down your esophagus to the stomach.  This can cause discomfort and irritation, but can also lead to increased potential for heartburn and reflux. (More on that in the next blog!)

On a chemical level, if your food is not spending enough time being broken down and mixed with saliva in your mouth, you are not going to get the benefit of two very important digestive enzymes, amylase and lipase.  Digestive enzymes are chemicals that speed up how quickly components in your food are broken down. Different enzymes help with different parts of your food.

Salivary amylase is a digestive enzyme secreted in the mouth that helps to break down carbohydrates into smaller sugars.  If you have ever put a cracker in your mouth and let it sit there for a moment, you will notice that it quickly breaks down to mush.  This is in large part a result of the amylase.  If carbohydrates are not getting broken down adequately, it can lead to carbohydrate malabsorption that can cause painful gas, bloating, and even diarrhea.

Lingual lipase is an enzyme secreted from under your tongue that helps to begin breaking down fat in your food. If you don’t take time to chew your food, the fat in your food may not be getting digested well which can also lead to cramping, bloating and heartburn.

So how long should you chew your food?

In the late 1800’s there was a health food proponent named Horace Fletcher who promoted the idea of chewing your food thirty two times before swallowing.  He declared that “nature will castigate those who don’t masticate.”   While there is no harm to chewing this much (except for possibly a sore jaw), there is no magic number of times you should chew your food.  The size of the bite and the type of food are going to affect how long it takes for it to be well broken down and mixed with saliva and enzymes.

Following these steps can help to make sure that you are chewing adequately:

  • Don’t bite off more than you can chew.  Taking smaller bites will decrease the number of times you have to chew.
  • In general it is a good idea to chew until the food feels like it is the consistency of a paste and is saturated with saliva.
  • If you find that your mouth is dry and you are not producing saliva this may be an indication that you are not yet in a parasympathetic state.  Put your fork down and take 5 to 10 breaths before proceeding. (See my previous blog for more details)
  • Finish chewing one bite before starting on the next. Placing your fork, spoon, or sandwich down between bites will help to slow you down and make it easier to do this.

In addition the benefits mentioned above, taking time to chew your food will help you to eat more slowly, allowing your brain time to register that you are full which will help to avoid overeating.  Eating more slowly will also help to keep you in the more relaxed or parasympathetic state which will enhance the entire digestive process.

Instead of thinking of summer barbecues as a time for more opportunities for indigestion, think of them as a time to practice your chewing and see if you can promote optimal digestion. In my next blog we will make our way down the esophagus to the stomach and see that stomach acid is not just a pesky annoyance that we should take purple pills to suppress.

The Road to Health is Paved with Good Intestines

iStock_000012048107Small-300x300When it is working well, most of us don’t spend much time thinking about our digestive tract.  We put food in our mouth, we may chew it a little bit, we swallow, and then its gone.  If all is well, we have a bowel movement or two a day and think nothing more of it.  We might feel a little grumbling in our stomach if we are hungry or we feel a little unsettled if we eat too much or too fast, but otherwise we tend to take our digestive tracts for granted.

Our gastrointestinal tract is a remarkable system.  It turns food into microscopic particles that can get absorbed into our blood stream and be used for energy, maintenance, growth, and repair. It has its own immune system.   Ideally it keeps out things that are foreign and harmful and allows in things that are safe.  It defends us from the bacteria, yeast, parasites, and viruses that are on everything that we put into our mouths.

However, it is not uncommon for our gastrointestinal function to be less than optimal.  It is estimated that 42 million Americans suffer heartburn on a weekly basis and 45 million suffer from irritable bowel syndrome.    We are bombarded with ads for pills that stop “evil” stomach acid and for yogurts and fiber supplements touted to promote regularity.

Why does one of our most basic processes so easily go awry? 

To help you have a better understanding and appreciation for your digestive tract and how to keep it happy, over this series of blogs I am going to take you on a tour of digestion and your digestive tract.  I will show you ways to keep it working well, or to get it back on track if necessary.


It’s All in Your Head

As we begin our tour of the digestive tract , you might think that we would begin with the mouth.  However, setting up our gastrointestinal tract for optimal digestion starts before a bite of food ever enters our mouths.  Even before the mouth, digestion really begins in the mind.  The mind is an often overlooked digestive organ and in my experience at the route of many digestive issues.

The thought, smell, or sight of food will actually cause our digestive processes to begin.  In response to the stimuli our salivary glands begin to produce more saliva, our stomachs begin secreting acid and enzymes and  the entire digestive tract begins to experience a wave like motion called peristalsis.

In addition, the mental state that we are in when we eat can have a profound effect on our digestive function.   For optimal digestion to take place we should ideally be in a relaxed state called a parasympathetic state.  This is in contrast to a stressed or sympathetic state.

Throughout the day and in response to external and internal stimuli, we shift back and forth between these two states.  The parasympathetic state is our relaxed state and is referred to as the rest and digest state.  The blood flow is going to the digestive organs to process the food that we are taking and promote proper motility of the gastrointestinal tract.

Evolutionarily the sympathetic state is the acute stress response.  You are confronted by a predator and you need to either run or fight.  This requires our blood supply and energy to go to the brain and to our arms and legs.  The response is meant to be short lived.  You get away, kill the predator, or get killed.

In our modern lives we are not confronting many bears or lions, but instead our stressors come in the form of traffic, work deadlines, the economy, family problems, money issues, and the 24 hour news cycle. Unlike being attacked by a bear, these are not isolated events, but instead tend to be constant.  Because of this, we tend to spend most of our time in this sympathetic state.

This effects our digestion because when we are in the sympathetic state blood flow is not preferentially going to our digestive tract and so it does not function as optimally.

Most of the time when we eat, we are not focusing on eating.  We are not aware of what we are putting into our mouths, and we are not in a relaxed state.  We are eating in the car, at our desks in front of the computer, while texting, while watching TV.

Before the food even enters into our mouths, we are setting ourselves up for impaired digestion.   Taking time to actually focus on the food that you are eating and allowing yourself to be in a relaxed state when you eat will help to get things started on the right foot.

While it can be difficult to shut everything off and allow ourselves to be in a relaxed state when we eat, there are simple steps that you can take to get yourself into a parasympathetic state and get your digestive process started on the right foot.


  • When you eat, eat! Before eating, turn off your computer and your television.  Put away your book, your newspaper, or the project you have been working on.
  • Your car is for driving and not for eating.  Wait to eat until you arrive at your destination, or stop and take the time to eat before continuing on your way.
  • To start your meal, stop and take 5 to 10 slow deep breaths.  This will help to clear your mind of distractions and also puts the body into a relaxed state that allows digestion to occur more optimally.
  • Take a moment to look at and smell your food before you begin eating.  If the food isn’t pleasing to look at and doesn’t smell good, it may not be the best thing to be putting in to your body.


By starting your digestive process off on the right foot, you will be more likely to digest your food well and less likely to cause yourself uncomfortable symptoms such as heartburn and indigestion.

In the next blog, we will enter the mouth, doorway to our thirty foot long gastrointestinal tract and see why your mother was right when she told you to chew your food.