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Gut Health - The Microbiome and Digestion - Part I

In this post, we are going to specifically look at how bacteria fit into this whole mix of surviving and thriving as a human and how they impact digestion.

At first glance, it might seem that the large intestine got the short end of the stick when it comes to digestion. Most of the breakdown of food and absorption of nutrients is already taken care of by the stomach and the small intestine.

So, what’s left for the large intestine other than being a wide tube for waste? As it turns out the large intestine may be home to one of the most important and overlooked functions. It houses the majority of your gut bacteria as well as all the organisms that comprise your microbiome. Very few microbes hang out in your small intestines due to oxygen, antimicrobial peptides, and lower PH levels. Plus, the shorter transit time in the small intestine makes the environment less hospitable to various bacteria.

In the large intestine or colon, leftovers from food are basically just hanging out due to slow transit time and fewer microbes. Bacteria also like to hang out in the colon because it folds over itself creating a lot of surface area for bacteria to attach. Bacteria can now break down or excavate the extra leftovers for fuel. Their favorite food is non-digestible plant fibers called polysaccharides.

Bacteria live in the lumen, the tube itself, and they attach to the mucosal lining which also doubles as a food source when you don’t provide enough veggies for your bacteria to munch on.

Okay, so you know what these bacteria like to eat, but what do they do? Why do we have them?

Your gut bacteria is the largest contributor to your metabolic process. It can regulate inflammation which as we know can lead to chronic disease and is essential for the development of your immune system, perhaps determining whether you develop allergies or autoimmune disorder. They may even be behind your cravings, your mood, and your behaviors.

But what if part of your cravings were due to your microbes in your gut? It might be worth taking a look at how we can create microbial changes. Bacteria are everywhere. There are more bacteria in our gut than humans on the planet and stool is 60% bacteria.

The bacteria in your gut help digest food, create vitamins, and modulate other functions in the body. Drugs and food are metabolized by gut bacteria if they make it down to the colon.

The bacteria serve as gatekeepers for things that we want to enter and all that we want to keep out. When you eat a vegetable, your body breaks the carbs down to glucose, but you will have some leftovers which are called indigestible fiber. What’s the point of this leftover fiber?

It’s not just useless mass, it turns out the digestive system is built in a really cool way so you can extract the most nutrients possible out of your food. All indigestible fiber is consumed by bacteria who act like little vacuum cleaners feeding on the fibers you can’t digest, and the bacteria, in turn, creates several molecules that provide nutritional value out of what you might have considered waste.

You can imagine how in times when food wasn’t so available this was really important. The body found a way to do this neat trick by populating the gut with trillions of bacteria that feed on indigestible fibers. When the bacteria feed on these fibers they carry out a fermentation process in the gut the same way sauerkraut or kombucha or beer is made, except this happens on the inside.

40-50% of the energy in carbohydrates is extracted by fermentation. This fermentation process creates molecules that can also help regulate body functions such as immunity, hormones, and inflammation.

Remember how we have hormones and neurotransmitters that send signals to our bodies to respond in this way or that, well the bacteria molecules send signals to our bodies too. They create some that help us and some that don’t, depending on what kind of bacteria they are and what they are eating.

Let’s go over some of the essential building blocks created by bacteria.

Essential building blocks created by bacteria include:

1. Vitamins – like vitamin B12 and K. Vitamin K can only be produced by bacteria.

2. Amino Acids – such as arginine and glutamine and they can regulate the uptake of amino acids like tryptophan

3. Short-chain fatty acids – these are not just the course of calories. Short-chain fatty acids play a role in down-regulating inflammatory pathogens and even have anti-tumor properties and they also help to build intestine mucosa. Butyrate is an example of a short-chain fatty acid which can also be found in foods like butter. This is why butter is included in many but healing diets.

The 3 main short fatty acids created by bacteria are:

a. Acetate

b. Butyrate

c. Propionate

4. Neurotransmitters – our bacteria create neurotransmitters just like the ones in the brain such as serotonin and GABA.

5. Enzymes – help breakdown more food

Bacteria metabolize bile acids and compete for resources with other bacteria, the harmful ones. In doing so it can starve the other guys out so it's advantageous to keep the good guys strong.

We’re learning that the same bacteria species can create different byproducts and metabolites. This leads some to believe that the food

we provide them might be more important than the type of bacteria themselves. Again, a supportive fact that what we eat matters.

So, who are these bacteria? The gut is filled with an entire ecosystem of bacteria. We’re only beginning to understand which bacteria do what and since the entire paradigm is switching to look at the ecosystem and how they operate as a whole we can’t look from a simplistic angle of one bacteria having one function.

There are two main categories of bacteria: Aerobic and Anaerobic

Aerobic bacteria are those that survive with oxygen and Anaerobic bacteria are those that survive without.

Aerobic bacteria tend to be more often pathogenic meaning they cause disease. The main bacteria in the gut fall into these 3 categories:

The 3 categories of gut bacteria:

· Firmicutes

· Bacteroides

· Proteobacteria

We are only now beginning to make connections between diet and the type of bacteria that seem to thrive on any given food source.

It does seem that various groups tend to predominate depending on the food source. For example, Firmicutes seems to thrive on a high-fat diet and dwindle when we fast. Bacteroides love a low-fat diet with tons of fiber. When there is a high ratio of Firmicutes to Bacteroides there seems to be a greater risk for obesity. Therefore, we can tell if someone is lean or obese just by looking at their microbiome. Good bacteria or a combination of bacteria in the wrong ratio can play a role as to whether we are obese or skinny.

In the latest experiments with mice, which is how many experiments start, scientists took bacteria from an obese mouse and placed it in a mouse that was free of bacteria. That mouse became obese. Even when they were given the same amount of food and exercise. The reverse can also happen.

Your gut bacteria can influence how various foods affect your blood sugar. This is why one person eats a banana, it can influence their blood sugar and for another person, there is no effect.

The key is in the microbiome. So, it is really important for us to understand this community and how it can alter our responses.

We’re discovering that Dysbiosis which just means an imbalance of your microbial community is present in many chronic conditions from Crohn's disease to autism. What we don’t know is which is the chicken, and which is the egg. But we do know that the more diverse your bacteria the healthier and more resistant your ecosystem. Not to be misleading because harmful pathogens will still exist in a gut with a diverse ecosystem.


But in a balanced ecosystem, these pathogens seem to exist in small amounts without causing any harm.

In the western world, we have about a thousand to twelve hundred different gut species which is a far cry from our ancestors. Why does diversity matter?

Imagine that one species gets killed off or dies of starvation, the body or any ecosystem needs an alternative species that can step in and fill that gap.

Our diverse gut bacteria easily switches between diets, vegetarian, carnivore and omnivore, which was an important ability during primitive life when people had to eat whatever was available

This is also why different bacteria can create the same essential by-products, all created for our survival. When diversity is low we are more susceptible to disturbances and diseases. This is troubling because the average person’s gut diversity has been dramatically changed or has been weeded out due to the Western diet, antibiotics, and other reasons we’ll cover.

But the good news is this is reversible. Another benefit of paying attention to bacteria is that can bacteria change really fast. What we eat alters the demographic in the intestines and therefore, our metabolism and cravings. For instance, vegetarians have more veggie digesting bacteria, alternately some folks don’t have the bacteria to breakdown carbs efficiently. However, when diets change some of these bacteria seem to pop back up as if they have already been waiting there.

The high fat, high sugar, and reduced fiber typical of the Standard American Diet (SAD) seem to correlate to a decrease in diversity. Less diversity may be a reason for the rise in many chronic conditions.

Dietary changes can alter gut bacteria for the short and long term. Dietary changes may occur rapidly, but it can take years to increase overall diversity and ratios of gut bacteria in the microbiome.

Another thing to be mindful of is that gut bacteria may determine whether a drug or supplement will work or how the body responds to it. For example, microbes in the gut can determine which pain killers are toxic to your liver.

Companies are already exploring how to utilize this information, for example, the Gates Foundation, is studying whether we can address malnutrition with peanut butter containing healthy microbes. It will be really interesting to watch developments unfold as scientists but their newfound knowledge of the microbiome to use.

When it comes to food and drug safety, we’ve forgotten to look at bacteria. For example,

Emulsifiers, binding agents that are included in many processed foods have proven safe in humans, but we are now realizing they affect gut bacteria. Studies show that emulsifiers in our food can kill species of bacteria in the gut that help build mucous lining. This is very bad news because the mucous lining provides protection against other pathogens. When this is disrupted our body responds with inflammation.

So, to recap the bacteria in the gut form several major functions, they help us extract more nutrients from our food while at the same time produce essential nutrients. They also send regulatory chemical signals that control functions such as hunger and motility. Lastly, they protect us against pathogens.

The microbiome is often referred to as the wild west. Scientists and experts are holding back from making definitive claims or promises about it because the more we know the more it seems we don’t know. If any information about the microbiome seems confusing know that this area is rapidly evolving and changing. In the big picture, it still hasn’t been determined whether the microbiome is an expression of disease or a potential cause. However, we are seeing that it does evolve and change with us and reflect our current state. As we suspected years ago, the gut still seems to be the center of health and in an epidemic of chronic disease, we’re also placing it at the center of our hopes.

Next week we'll continue with our Introduction to the Microbiome and discuss:

The Microbiome and Digestion- Part II


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