Favorite Articles


The Gut Zoo

Your body is home to a wide variety of creatures too small to see. A large number of them live inside your gut and create a kind of inner zoo. This gut-zoo has far more creatures living in it than any actual zoo you’ve ever visited. Together these creatures play a crucial role in the health and welfare of your body.

While it is predominantly bacteria that populate our gut-zoo, some fungi, and even viruses, can set up house in the digestive system. Most people know their guts house bacteria, but many are unaware of how important they are to overall health.

What Do Bacteria Do?

These gut bacteria are far from passive bystanders of our guts. We give them a home, and they provide us with many benefits. It’s a symbiotic match made in heaven – a relationship where both organisms benefit.

1. Developing Gut Flora:

The bacteria that inhabit the gut early in life help the cells of the gut grow and develop. They also help to train the immune system. The gut flora actually work in concert with the immune system in order to help it grow and develop, and to help fight bacterial and other infections as we mature.

There is some evidence that the bacteria in the gut help to stimulate and help to train the immune system.3 There is also some intriguing new research that supports the theory that gut bacteria can have a calming effect on an overactive immune system. This creates hope for the possibility of new ways to reduce asthma and eczema.

2. Digesting Food:

The various sections of the colon contain different bacteria and they each have distinct jobs. The bacteria in the first part of the colon help to ferment and digest carbohydrates, and the ones in the latter part of the colon help to digest fats and proteins.

The most beneficial of the digestive processes appears to be had from the digesting of carbohydrates; much of the nutrient value we derive comes from the ability of bacteria to digest hard-to-digest carbohydrates. Your body can only digest so many carbohydrates. Therefore, any carbohydrate such as a fiber, which is too difficult for us to digest – or any carbohydrate that simply wasn’t digested earlier in the digestive tract – becomes food for the bacteria in the colon.

3. Deriving Nutrition:

Since the bacteria in the colon are digesting foods that were missed earlier in the digestive process, they are helping us to absorb nutrients that would not otherwise have been absorbed. In a way, the bacteria in the colon represent a second stomach and digestive enzyme system.

As these bacteria are munching on food, they help us absorb key vitamins such as biotin and vitamin K. They also help to balance water in the gut.

4. Policing:

One of the most important roles bacteria play is keeping undesirable bacteria and fungi (yeasts) in check. Healthy bacteria produce toxins that make it hard for bad bacteria like Clostridium to grow.

Harmful bacteria and yeasts grow when there is not a strong population of good bacteria around. In fact, experimentally, animals with low amounts of good bacteria are very easy to infect with bad bacteria.5

Good bacteria compete for food and attachment sites (areas in the gut where bacteria are capable of implanting), and actually produce toxins that are harmful to the invading bacteria; this keeps the population of bad bacteria low. Acidophilus, for example, produces hydrogen peroxide which is directly toxic to many bacteria.

Candida is harmful yeast that can grow out of control, and become detrimental to the gut. Having a strong gut ecology can eliminate problems with candida.

Your Gut’s a Bacteria Zoo

Infants are born without any bacteria in their guts. They acquire them through their mother’s birth canal, or via breastfeeding. Bottle fed infants acquire bacteria through the food they eat.

Scientists who study bacteria in human feces (how would you like to have that job?) estimate that there are somewhere between three hundred and one thousand different kinds of bacteria inhabiting the gut.1 Of these, approximately thirty or forty different species make up the bulk (ninety percent) of the inhabitants. Researchers believe that these thirty or forty species are the most important to gut health. These include Bifidobacterium and lactobacillus Acidophilus, among others.

If you could count all the bacteria in your gut, you would find that they outnumber the total number of cells in your body by a large number. The cells that make up your body (heart, liver bone, and brain cells) add up to around 1013 cells (10,000,000,000,000). The bacteria in your gut outnumber the cells that make up you ten to one.

By far, most of these bacteria are found in your colon. It is estimated that together, all the bacteria in your gut weigh between three and five pounds. Each bowel movement contains a large amount of these critters, with one to two-thirds the dry weight of stool being solely bacteria.2

Good versus Bad Bacteria

The populations of bacteria that live in your gut are a combination of both good and bad bacteria. And while you might think that you would want to get rid of all the bad bacteria and keep only good bacteria, it is actually the balance between the good bacteria and bad bacteria that is considered the healthiest.

The good bacteria are bacteria such as Lactobacillus acidophilus, Lactobacillus bulgaricus, Bifidobacterium bifidum, and others. The good bacteria help us digest food, maintain a healthy gut, provide us with nutrients and vitamins, and fight off bad bacteria. These good bacteria can be taken as a probiotic supplement.

Bad bacteria become problematic when their numbers grow too large in proportion to that of the good bacteria, and this is when they begin to create health problems. Bad bacteria include those which cause disease such as Salmonella, Clostridium, and others. Even yeasts such as Candida are fine in small amounts; they only become problematic when their numbers increase uncontrollably.

Damaging the Ecosystem

The ecosystem of the gut is important to your health. The problem is that it is very easy to disturb this ecosystem and create an imbalance. In a normal gut, the good bacteria will hold the bad bacteria in balance. Tip the balance and the bad bacteria and yeasts will grow and multiply, causing all sorts of health problems.

The most common way to upset the balance of good and bad bacteria is the use of antibiotics. The good bacteria in your gut are very susceptible to damage caused by antibiotics.

Other things that can damage good bacteria include ingesting too much sugar and processed foods, alcohol, drugs, and even stress. Toxins in our environment – including food preservatives, additives, and colorings – all make it difficult for the good bacteria to thrive.

Gut Bacteria and Conditions

A whole host of health conditions can be traced back to poor gut ecology. Gut problems, including gas, bloating, constipation and Chrons,  Irritable bowel symptoms (IBS) and ulcerative colitis can all be improved through a better gut ecosystem.6 A good ecosystem is linked to less colon cancer.7 Even diseases such as asthma and arthritis are thought to be linked to gut ecology.8

Interestingly, studies have also shown that gut bacteria may contribute to weight gain. While new information is just beginning to be gathered, it appears that bacteria in the colon may produce chemical messengers (called leptins) that let us know when we feel full. A disrupted colon ecosystem sends messages to the brain that tell us we need to eat more when in reality we have already eaten enough.

Repairing the Intestinal Ecosystem

It might seem as though repairing the ecosystem would be easy. All you’d have to do would be to take some of the good bacteria and you’d be set. While this is true to some degree, there is a much more comprehensive approach that can be taken. It is not just about replacing the good guys; it’s also about rebalancing the bad guys.

Step One: Bring in the Good Guys

You need to replace the good bacteria in your gut. There are too many things in our modern world that make it difficult for healthy bacteria to survive. If you have taken antibiotics recently, been under a lot of stress, or are eating poorly, then you need to consider taking probiotics.

Step Two: Up the H20

In case you didn’t know it, stool is comprised of seventy percent water. You need to make sure there is enough water in your gut so that the bacteria can do their job, and be easily expelled in feces. An added benefit of having enough water is to help avoid constipation. Bacteria thrive in an environment where there is plenty of room to move around. Constipation produces stools that are hard and compact, creating an environment in which it is difficult for healthy bacteria to thrive.

Step Three: Reduce the Bad Bacteria

The best way to reduce bad bacteria is to use a colon cleanse comprised of herbs that have been shown to reduce these bacteria. In order to ensure the health of your colon, performa colon cleanse several times a year.

Step Four: Reduce Stress, Increase Food Quality

You can do your gut a favor by reducing the amount of stress you have, and increasing the quality of the food that you eat.

The relationship between stress and the stomach is a complicated one, but most people notice some change in their bowel habits when they are under stress. Practicing yoga, meditation, prayer, or any other form of stress reduction can greatly benefit the gut.

Since food is what you and the bacteria in your gut gain nutrition from, it makes sense to put the best food possible into your body.


1. Sears CL. A dynamic partnership: celebrating our gut flora. Anaerobe. 2005 Oct;11(5):247-51.
2. Guarner F, Malagelada JR. Gut flora in health and disease. Lancet. 2003 Feb 8;361(9356):512-9.
3. Sears CL. A dynamic partnership: celebrating our gut flora. Anaerobe. 2005 Oct;11(5):247-51.
4. Björkstén B, Sepp E, Julge K, et al. Allergy development and the intestinal microflora during the first year of life. J Allergy Clin Immunol. 2001 Oct;108(4):516-20.
5. Sears CL. A dynamic partnership: celebrating our gut flora. Anaerobe. 2005 Oct;11(5):247-51.
6. Guarner F, Malagelada JR. Role of bacteria in experimental colitis. Best Pract Res Clin Gastroenterol. 2003 Oct;17(5):793-804.
7. Guarner F, Malagelada JR. Gut flora in health and disease. Lancet. 2003 Feb 8;361(9356):512-9.
8. Hart AL, Stagg AJ, Frame M, et al. The role of the gut flora in health and disease, and its modification as therapy.Aliment Pharmacol Ther. 2002 Aug;16(8):1383-93.
9. Ley RE, Turnbaugh PJ, Klein S, et al. Microbial ecology: human gut microbes associated with obesity. Nature. 2006 Dec 21;444(7122):1022-3  10.Dr. Scott Olson ND

Leave a Comment