For a working microbiome - Yogurt is not the best solution

The Human Microbiome – A Working Rental Agreement with Bacteria

Are Bacteria Bad?

Most bacteria are helpful and essential to our health. Our bodies have large spaces, mostly in our large intestines, that we in effect rent out to bacteria. These spaces host ten times more bacteria than we have cells in our body. This rental arrangement is called a working microbiome and greatly benefits both parties.

It functions like this—we provide bacteria with comfortable quarters and food flowing through their homes. This food in our eyes is not the best. It’s mostly undigested carbohydrates, fiber and protein by products. The food we could digest has already been absorbed in the small intestine.

In return for a home and food, bacteria break these difficult human foods into energy, vitamins, healthy fats and new proteins. The bacteria can do this because they each have their niche enzyme system that allows them to handle specific foods the digestive system and most other bacteria can’t. The new food created by these bacteria gets shared by the host (us) and the bacteria.

As we are finding out how beneficial some bacteria can be we have had to change our views. Even hospitals, that previously strove to eliminate all bacteria, are now trying to harness bacteria to restore a working microbiome for their patients. See Contributions of Intestinal Bacteria in the Critically Ill for more information.

Do We Need Sterile Conditions?

In the last two centuries we have paid a lot of attention to the bacteria that kill us. We have focused on the benefits of sterile conditions for wound care and antibiotics to kill bacteria and cure illness. This attention has become generalized to the point where we have attempted to eliminate all bacteria with anti-bacterial soaps, disinfectants etc. Now current research tells us that moderation applies here too. Sterile conditions means no working microbiome and prevents the “good” bacteria from keeping the bad ones in check.

There are special laboratories that grow germ free rats and mice. These animals have no bacteria in their digestive tracts or on their skin and are kept isolated in special cages much like the “boy in the bubble” but more so. They don’t get any diseases but their lack of a working microbiome makes their intestines smaller, distorted and less effective. These animals also need need extra water and  food to stay healthy. Even their nervous systems grows differently in sterile conditions in a way that leaves the animals more prone to stress.

Pea root nodules, a microbiome

Do Plants Host Bacteria?

Rhyzobium Bacteria lives in and distorts the roots in legume plants. This invading bacteria enters the roots and forms the round swelling you see in the picture on the right to create a comfortable home. They also tap the sap running through the roots for nutrition. This sounds bad, but these bacteria are not free loaders, they convert nitrogen gas from the air into ammonia, a nitrogen fertilizer. Plants can’t do this for themselves but they benefit from the bacteria providing them a supply of ammonia, which is essential in making protein.

Such plant-bacteria relationships are called a symbiotic. Plants provide a home and food, bacteria provide ammonia that helps plants grow and make protein rich seeds. This relationship is another example of a working microbiome. It’s so beneficial that gardeners buy bacteria in dried form to add to soil when they plant their seeds. It’s called a soil inoculant and is widely used.

Cows Can’t Digest Straw?

Cows and other ruminants are totally dependent on bacteria. They need bacteria to digest the grass and straw they eat. A cow raised  without bacteria would die of starvation. Cows and other ruminents therefore provide bacteria with premiere accommodations—the rumen. In a cow it’s a 50 gallon stomach designed for and filled with bacteria. There, bacteria break down the cellulose, pectin, and other indigestible parts of grass and hay. Only when the grass and straw have been converted to small particles of partially digested fiber, healthy fats, proteins, and vitamins, does it travel to the second stomach. Renting out the rumen to bacteria creates this great working microbiome and allows cows and other grass eating animals to survive on foods they cannot themselves digest.


How do Bacteria Benefit us?

Bacteria in our large intestines break down foods we can’t digest. They’re not as specialized as those in the cow; they can’t break down the cellulose in grass and straw but they help digest foods we can’t and produce healthy fats, some amino acids and vitamins like B1, B2, B4, B5, and K.

The bacteria in our intestine need an environment without oxygen. Most belong to two bacteria families:

  • bacteroidetes are versatilethey handle all kinds of fibers from beans to complex starches—bacteroidetes for a lean body
  • firmicutes are efficient—they can wring the last calorie out of basic foods like starch and fat—famine favors firmicutes

Efficient bacteria are good when there’s a famine but in our high calorie world it’s much better to have more versatile bacteria.

How do Bacteria Effect Caloric Intake?

Studies have shown that overweight people tend to have mostly efficient firmicutes bacteria, this is true for mice too. By changing the balance, increasing the versatile bacteroidetes bacteria, both people and mice loose weight in the short run. These short term weight losses are due to the the new versatile bacteria that were added to the large intestine. The effect lasts only a short time unless the versatile bacteria can stay and thrive.

A more long lasting and easier way to increase the versatile and decrease the efficient bacteria is to increase the fiber in the diet and limit fat, sugar and processed foods to a small part of your daily calories. The opposite is also true. Start eating a lot of junk food and you’ll increase the efficient firmicutes population, making it easier to gain weight.

Imagine the large intestine as rental housing. Provide nice accommodations—lots of fiber and low amounts of junk food—and you attract good tenants. But if you switch to junk food only seedier tenants will stay.

What about Fecal Transplants?

Our intestines are colonized mostly at birth from bacteria that come from our mothers. These bacteria and their progeny stay with us for the rest of our lives. Just the relative proportion of the various bacteria shifts in response to long-term diet and antibiotic use.

Antibiotics kill intestinal bacteria. Unfortunately, bad bacteria like c. difficile are immune to many antibiotics. These dangerous bacteria exist in our intestines in small and harmless numbers as they can’t compete with the other bacteria. When other bacteria are killed with antibiotics things change. All of a sudden these bad actors can flourish and wreak havoc in our intestines. Sometimes after taking antibiotics the usual bacteria are so badly decimated they can’t stage a comeback and the digestive system becomes a painful mess. This is when fecal transplants are helpful. A healthy person’s intestinal bacteria are introduced to the damaged large intestine where they quickly colonize it and out-compete the dangerous bacteria that are causing all the pain and damage.

If the person receiving a fecal transplant already has a full compliment of mostly efficient famine favoring firmicutes, the transplant just adds some desirable tenants to a full housing complex. Not everyone can stay and who stays depends not on who you brought in but on the housing conditions. Are you providing a varied diet rich in fiber or is it high in sugar and fat?

What Are Prebiotics?

cutesy of Wikipedia commons

Prebiotics is a fancy term for fiber and the complex carbs that we need bacteria to digest for us. These are the foods that encourage better tenants for your intestines. There are many such fortified foods available, but prebiotics are better supplied by fiber-rich foods like legumes, whole grains, vegetables and fruits (but not their juices). These foods give you a greater variety and larger amounts of fiber that attract more versatile bacteria.

Foods labeled fiber and prebiotic are popular with food processors but that does not make them healthy. The latest ludicrous example is Coca-Cola plus fiber—it has been fortified with dextrin, a fiber that is commercially made from starch. This fiber is clear, slightly viscous and without a gritty texture—it is the most common way to fortify foods with fiber. But fiber is not just one thing—there are at least six different forms of fiber, some soluble, others not, and each has a different role (see comparison of different fibers). Let me assure you that an apple is  a better choice than Coca-Cola plus fiber.

How do Probiotics, like Yogurt, Work?

Probiotics are foods and supplements that contain live bacteria that help digest food. They’re useful if you’ve lost your bacteria or are taking antibiotics that are killing your good bacteria. What they don’t do is replace the bacteria already in your intestines, they just help those bacteria stage a comeback after they have been decimated.

Probiotics, like the live bacteria in yogurt, are not big players in the intestinal tract. What they do well is create an acidic environment around themselves that harmful bacteria don’t like. They’re good bacteria to have in the intestines but they are not going to shift your bacterial tenants from efficient to versatile. They also do not make you more regular (unless you are on antibiotics), for that you need insoluble fiber, not the dextrin found in fortified foods!

What’s the Takeaway?

If you look at my previous posts you see that I have been encouraging healthy diets, like the Mediterranean diet, that have stood the test of time for centuries. These historical diets are rich in legumes, fruits, vegetables, and whole grains, making them ideal if you want a versatile working microbiome.

Now we are seeing more scientific data that explain why these diets are so good for us. For best results make changes gradually. Try to add legumes to your diet a few days a week, and choose whole instead of refined grains at a few other meals. Add an extra vegetable to your meals and soon you too will be encouraging the versatile bacteria to dominate in your intestines.

Let me know how trying these diet changes helps you.