Tuesday, October 8, 2013

Your Lactobacillus is Showing: A New Way to Look At Poop

After decades of eating grains, legumes, laboratory-produced additives, and a lot of miscellaneous junk, our gut health is gradually pooping out (see what I did there? I'm so punny).  It took a while, but probiotics are finally on the lips of vitamin shoppers and health foodies around the world.  These capsules of live bacteria have worked wonders for millions with a wide array of resistant health issues.
The human gastrointestinal (GI) tract

As it turns out, the integrity of the lining of your gastrointestinal (GI) tract is extremely important for your overall health.  Who knew?!  Despite this topic lying largely on the fringe in the conventional medical community, gut lining inflammation has been of interest to researchers since the 1980s.  This lining has built-in mechanisms  to help it withstand years of abuse from what we eat, but, over time, these mechanisms begin to falter, and the results can be devastating.  The main players in keeping your gut healthy are the trillions of bacterial and fungal flora living there.  They aid in the digestion of nutrients for easy absorption as well as attenuating the effects of harsh compounds on the gut lining.  If we want to remain healthy, we need to keep the flora healthy, and this is where Sweat and Butter enters the picture.

In this post, I hope to accomplish three things:

1) Describe the role of bacteria in keeping us healthy.
2) Examine the impact of poor diet on these bacteria.
3) Describe the conditions that may result from poor gut health.
4) Provide recommendations on how to replenish your gut flora.

Bacteria in your body
Your body is comprised of between fifty and one-hundred trillion human cells - that's 100,000,000,000!!!  Can you even believe it?!  The number of bacteria that we provide a home to outnumbers human cells 10-1.  These little guys line your mouth, nose, airways, esophagus, the intestines, skin, hair follicles, eye balls, ear drums, and then some.  While most people generally think of bacteria as harmful, they actually serve some very important roles in our body, particularly in the gut. 

Bacteria often have the ability to digest raw materials better than the cells lining our intestine.  In fact, many food molecules that we eat require some level of processing by bacteria living in the gut in order to be absorbed into our blood.  Fascinating!  

The bacteria that live in your intestines are accumulated at a young age.  A newborn's GI tract is largely unpopulated by bacteria, though breastfeeding rapidly introduces a variety of bacterial species.  Breast milk also supplies the infant's populated gut environment with simple sugars to help foster growth and multiplication of these flora.  As an infant begins to eat more foods and is exposed to different environments, the gut floral species shift towards a perfect balance of between 500 to 1000 different species.  This variety of species in specific proportions to one another serves an important role in digestion while simultaneously protecting your gut by maintaining the mucosal barrier, which is your first line of defense against invaders that enter our body through food.

Not all of the bacteria in your gut are beneficial.  The species of bacteria that aid in digestion are probiotics, meaning they promote health.  They are also important for keeping pathogenic, harmful gut bacteria in check.  The probiotics feed off the food that you swallow.  If you eat or drink the wrong stuff, the balance of probiotic to pathogenic bacteria becomes deranged, and your health suffers.

We can explain virtually everything in human physiology through an evolutionary biologic filter.  Humans and bacteria co-evolved such that both parties mutually benefited.  Sort of like: "Hey bacteria, if you help me digest polysaccharides, I'll give you safe harbor.  Deal?"  Bacteria wouldn't say much in response because they're bacteria, so they can't talk, silly. This intimate romance between our gut and the bacteria's need for a safe home is reflected in the fact that certain species of gut bacteria digest sugars in the mucus produced by the cells lining our intestines.  The volume of mucus is regulated by these bacteria, and, in exchange, the bacteria go to bed happy and fed.

Clinical research on the role of intestinal flora in maintaining healthy physiology and biochemistry is still premature, but studies thus far suggest that probiotic bacteria play a variety of roles in maintaining the health of your digestive system.  In addition, these microorganisms are also thought to influence energy metabolism (to the left, to the right, up top, down low, too slow) and nutrient absorption (shake, shake, shake, señora), particularly iron, B12, Vitamin D, and folic acid.  If the balance of good to bad bacteria gets jumbled, it is reasonable to assume that the imbalance may carry negative health consequences.  More on this later. 

Bacteria have needs, too, ya know... 
Because the inside of your intestines is devoid of oxygen, the bacteria living in your gut are unable to break down fatty acids, a process known as oxidation (oxi = related to oxygen). Bacteria thus preferentially eat carbohydrates, and they're particularly hungry for fiber and fructose. 

Here's how it works.  When you eat a meal, a lot of stuff is absorbed in the small intestine, including simple sugars.  The remaining fecal matter passes to the large intestine (aka the colon) where fiber - abundant in fruits and vegetables - is fermented by the trillions of bacteria that call the colon home.  What remains from this breakdown process are short chain triglycerides (aka fatty acids) such as butyrate, which can be absorbed and used by tissues around the body as fuel.  The process of digesting fiber provides your body with energy at a slower rate than eating sugars, which, as I mentioned, are absorbed readily in the small intestine - no bacteria required. 

As it turns out, the process of metabolizing fiber alters the varying proportions of bacterial species in the colon, and this can be a problem.  Medical researchers don't fully understand the specifics yet, but one theory is that overfeeding your gut bacteria increases the rate at which they multiply.  An excess of fuel for the bacteria - fructose and fiber - may shift the balance in such a way that pathogenic bacteria are permitted to multiply beyond the control of the probiotic bacteria.  When pathogenic bacteria die, they release endotoxins, so more bacteria means more endotoxins.  These endotoxins have been implicated in metabolic syndrome, liver disease, heart disease, and other inflammatory conditions.  No bueno.  More on this here.

When things go awry
Anything that we do to the environment inside of the gut - that is, the stuff that we put into our intestines in the form of food - can harm us indirectly by disturbing the peace amongst the thousand or so species of bacteria residing in our intestines.  If you have ever been treated for a few weeks or months with oral antibiotics, you may recall developing diarrhea.  Certain pathogenic strains of the intestinal flora - namely Clostridium difficile (C. diff) - are permitted to flourish under the influence of high dose antibiotics.  This pathogenic overgrowth causes a host of gastrointestinal problems including a horrible, stinky diarrhea. 
This is your gut lining under a powerful microscope.

Fortunately - or unfortunately, depending on how you look at it - the complications of C. diff arise shortly after the antibiotic treatment, and your doctor can respond accordingly.  It's easy to see the relationship between gut flora and your health in this case.  On the other hand, when diet leads to pathogenic bacterial overgrowth or if it knocks out your probiotic bacteria, it may take years for you to become very very sick.  On the other hand, you may have no clue that you aren't performing optimally if your gut flora have been deranged for decades.  It's difficult to diagnose imbalances in gut flora because there are few specific symptoms.  If, in fact, the probiotic gut flora are important in the processing nutrient absorption in addition to keeping the pathogenic (bad) bacteria in check to maintain the intestinal lining, the health of your intestinal environment is as critical to your general health as the food you put into it.  

A study conducted way back in 1983 concluded that rodents who had their gut flora wiped out required 30% more calories than rodents with normal, healthy gut flora to maintain body weight.  Furthermore, gut flora are thought to be involved in the regulation of body fat.  As I mentioned previously, clinical research on the role of gut bacteria is still premature.  Many researchers have observed that the gut flora of obese individuals differs from that of lean individuals, but the evidence is insufficient to conclude any causal relationship.  In other words, the intestinal floral make up of an individual may reflect their body composition or it may be the cause of their body composition.  This is a sexy topic in medical research right now, so more evidence is on the horizon.  For now, suffice it to say that even if you aren't experiencing diarrhea or heart burn, your gut may still be struggling with inflammation or an imbalance in gut floral species.

The underlying mechanism by which an imbalance in gut flora causes health problems is related to inflammation of the gut lining.  Remember: probiotic bacteria protect our gut!  If this lining is disturbed, small holes will allow endotoxins produced by the pathogenic bacteria as well as undigestible proteins contained in our food easy access to our bloodstream.  This scenario is commonly termed "leaky gut syndrome", and it can carry grave consequences.  

Some other health conditions that may improve once you get your gut flora under control are autoimmunity (including eczema), inflammatory bowel diseasenon-alcoholic fatty liver disease, inflammation, diabetes, Alzheimer's dementia, and bacterial vaginosis.  

Control the bacterial burn
It's reasonable to assume that fixing disturbances in gut flora may lead to improvement of these conditions, and this is an increasingly hot topic in medical research.  The foul-smelling condition I mentioned before, C. diff infection, is normally treated with IV fluids and additional antibiotics targeted specifically towards this pathogenic strain of bacteria.  In  addition, fecal transplants are increasingly being tested as a viable solution to severe C. diff.  The procedure sounds archaic, but clinical studies have shown overwhelmingly positive results. Basically, a clinician will get a large sample of stool from a patient with healthy gut flora and perform an enema to deliver this sample into the intestines of a patient with severe C. diff.

Replacing the sick patient's flora with the gut flora from a healthy patient seems to work, but it's a pretty radical procedure, and it could make a person pretty sick if they don't tolerate the transplant.  We simply can't say whether or not fecal transplants are a plausible treatment option in any condition other than C. diff infection.  I'm sure you are just aching to receive an enema of a stranger's stool, but, before you call your doctor for a session, let's first try to fix your gut floral derangement through lifestyle modification.

The state of gut flora is most heavily influenced by our diet, so eating foods that support the amount and quality of these flora is critical to your health.  Even people that aren't having diarrhea, indigestion, heart burn, etc. will likely benefit from the recommendations below:

1) Replace your probiotic gut flora
Image from paper by Qin et al;
accessed via

Oral supplements:
Probiotic supplements can be picked up in any health food store; however, it's still unclear which probiotic strains are the most beneficial in your quest for the perfect supplement.  Quite frankly, I'm not sure if any specific probiotics supplement is going to be perfect for everybody.  Clinical studies have examined the effects of supplementing with various combinations of different bacterial species.  Some studies have tried multiple strains of lactobacillus.  Others have looked at combinations of lactobacillus, bifidobacteria, and streptococcus.  The point is that these supplements, which come in oral form, have been poorly studied, though I don't foresee them having any negative effect on your health if you try them out.  Look for high quality brands that require refrigeration.  You need live cultures of bacteria!  So if it has a long shelf life at room temperature, it's probably not the best choice.  One brand our clients have found great success with is Garden of Life.

Fermented foods: An even better source of probiotics is fermented foods.  While probiotic supplementation will likely show some benefit, there are far too many strains of healthy bacteria found in the gut to fully supplement through oral capsules. Regardless of whether you decide to take oral probiotics supplements, you'll likely find even greater benefit from eating probiotics-rich foods.  Sauerkraut, kimchi, and kombucha are great sources.  They tend to have an acidic, vinegary taste, which turns a lot of people off, but give them a shot and you'll eventually acquire the taste!  Your gut will thank-you.

**Note: We don't recommend dairy for daily consumption, but if you find a raw yogurt source near you that adds live cultures, this might serve as a good last resort.  Major store brands of yogurt are sadly loaded with sugar and likely don't contain that much variety in the bacterial strains that they add to their products. 

2) Avoid fiber supplementation and excess fructose consumption
Instead of mixing up one of those nasty shakes of expensive fiber powder, get your fiber from fruit, vegetables, and tubers.  While several large studies in the past have found a positive benefit from fiber supplementation, a basic understanding of the digestive process suggests that this increases the potential for bacterial overgrowth.  Remember, bacteria eat fiber, so feeding them too much may cause them to reproduce too rapidly.  In fact, a condition known as SIBO (small intestine bacterial overgrowth) is treated adjunctively by limiting the amount of carbohydrates and fiber in the diet. You should also avoid eating too much fruit, which is loaded with fructose.  In addition to fructose's tendency to drive fatty liver disease and diabetes, it is also a preferential food for gut bacteria.  We want our intestinal friends to be full, not overstuffed!

3) Avoid gluten, legumes, dairy, alcohol and vegetable oils
Wheat, legumes, and dairy contain proteins that our gut has a hard time digesting.  Because we can't digest them, they cause inflammation to the gut lining.  Vegetable oils are rich in omega 6 fatty acids, which are inflammatory in and of themselves.  Excess alcohol consumption also has a direct inflammatory effect on the intestinal lining.  Remember, inflammation is public enemy number one.  This gut inflammation ultimately causes the gut lining to become leaky (read more above), and it allows stuff - including the endotoxins produced by gut bacteria - to enter your blood.  The gut flora protect your intestinal lining, which is why we are trying to balance this environment in the first place.  Does it make sense to fuel the inflammatory fire even more?  (That's a rhetorical question.)

4) Manage stress in your life
Stress leads to inflammation everywhere, including your gut.  If you are chronically stressed out, your gut health is likely less than optimal.  Research hasn't concluded that the link is solely due to a derangement of the floral species or increased propensity for gut lining inflammation.  A combination of both is likely to blame.  Even without sufficient clinical evidence, though, it's clear that there is some link between anxiety and digestion.  Think about those days when you aren't sleeping well, you are working on hitting deadlines, etc.  You tend to eat inflammatory foods (processed junk, gluten-rich foods, etc.) and your digestive processes don't function optimally.  Keeping stress in check (including getting sufficient sleep) is important for maintaining gut health.

Hopefully this guide has served to elucidate some of the confusion around probiotics.  As always, let us know if you've benefited from supplementing with probiotics or increasing your fermented food intake. Though, I have a feeling that we already know the answer to that...

Nathan Riley is a 2014 MD candidate at Temple University School of Medicine.  He writes about food, movement, sleep, relationships, and stress in order to bridge the gap between his patients and evolutionary theory and clinical evidence. You call follow him on Twitter @BeyondtheMD. He can be reached at

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