Suppose you decide to make health your hobby. You consult a top preventive-medicine doctor. “Doctor, I already do the dynamic duo, diet and exercise. Is there something more I can do to stay healthy?” The doctor says, “I congratulate you on taking charge of your life by making health your hobby. How’s your microbiome?” “My what?” “It’s the organ in your body that is one of the most important, but the one you probably know the least about. Most of the patients I see have messed up microbiomes. By maintaining a healthy microbiome, you maintain your health.”

Dr. Self-Care scribbles on a prescription pad:

Microbiome (also called microbiota, or “little life”) is now the number-one rising star of medical research topics and is the basis for one of the most doctor-recommended home medicines—probiotics. Get to know your microbiome! “Microbiome” is the community of microorganisms, mostly bacteria, that reside mostly in your gut. In return for free food and a warm place to live, they do good things for their host.

You will be surprised to learn what a powerful influence your microbiome has on your total body health. There is strength in numbers. These microscopic bugs outnumber our own human cells ten to one. (Obviously, they are very tiny compared to most of the body’s own cells.) Your microbiome is the biggest zoo in the world. An estimated 100 trillion bacteria reside in your gut, most of them in your colon, where more than a billion bacteria live in just one drop of intestinal fluid.

These bugs weigh a total of around three pounds, making your microbiome one of the largest “organs” in your body.


If you want to grow a healthy gut garden, you need to do three things: plant the best seeds, feed and fertilize the soil, and keep the weeds and pests out. That’s what a microbiome-focused diet does.

  • You plant the seeds (good bacteria) by feeding the gut lining (the soil) the foods it needs—high-fiber foods.
  • You fertilize it with a healthy diet.
  • You keep the weeds and pests out by eliminating junk foods. Having lots of good gut bugs helps with pest control.

The lining of your gut has trillions of microscopic parking places. If the good bugs fill up the parking places, there’s no place for the bad bugs to park and they simply get eliminated, pooped out. The best way to keep the bad bugs out is by encouraging more good bugs to grow, and that’s what a healthy, balanced diet does.


The “second brain.” Your microbiome’s influence extends from your bowels to your brain. The better we treat our microbiomes, the happier our minds. Call it your mind–microbe connection. Scientists call the gut “the second brain,” because it has the most nerve cells of any organ other than your brain.

The gut brain is connected to the head brain. Throughout human history, the head brain and the gut brain have had a great working agreement for keeping each other, and the rest of the body, healthy. The gut brain says to the head brain, “You’ve got to control those toxic thoughts—stress—that give me the queasies. The more relaxed I am, the better I can process the nutrients you need.”

So the head brain honors that request as best it can, and also prompts the human to eat real foods. That wasn’t hard, since real food was all there was back then.

Then, very recently in human history, four radical unhealthy-living changes occurred:

  1. The way we birth and feed our babies.
  2. Children moved indoors where they sit rather than go outdoors, play, and get dirty.
  3. The excessive antibiotics we give our children.
  4. The artificial foods we invented. Your second “personal pharmacy.”

The underlying theme of a balanced diet rich in gut-fortifying foods is tapping into your own personal internal-medicine pharmacy to make your own medicines. There’s an “internal pharmacy” in the lining of your blood vessels. Meet “internal pharmacy” number two, the one in your gut.


Your gut is sensitive. Just as your head brain feels good when it thinks good thoughts, the gut brain is programmed to feel good when you eat well. One of the earliest gut feelings you may have after a few weeks eating this way is, “That big burger bothered me.” Good! It’s supposed to! Your gut is now re-sensitized, transformed. Here’s what your microbiome can do for you:

  1. Keeps bad bugs out. Your microbiome fights the bad bacteria that enter your gut, keeping them from getting settled.
  2. Prevents leaky gut. Your microbiome makes intestinal paints, sort of sealants (immunoglobulin A and butyrate) to keep invaders and foreign particles from leaking through the intestinal lining into the bloodstream.
  3. Digests leftovers. Your body does not like to waste food. So your microbiome lives off the leftover food that your stomach and small intestine can’t digest, such as that chewy, fibrous asparagus stalk. 
  4. Sends biochemical messages to other organs. Your microbiome communicates with other systems, especially your brain and immune system, to tell these systems how to behave. When this was discovered, the microbiome’s status was upgraded to “the newest organ of the body.”
  5. Dispenses nutritional “medicines.” Your microbiome turns food leftovers into nutrients your body needs, such as vitamins B and K, and others. It’s especially important in making medicines your intestinal lining needs to heal and grow, nutrients you don’t get enough of in your diet. Microbial balance. Balance is critical to our health in many ways.

For example, the maturing immune system has to learn how to fight germs to keep from getting infectious diseases, but not to “overfight” and attack your own tissues; that causes autoimmune diseases like allergies and asthma. Food allergies have increased 50 percent in the past decade, and one of the triggers for this is thought to be a microbial imbalance.

You will always have healthy and unhealthy bugs in your gut. The goal of intestinal self-care is to make sure the good microbes far outnumber and outfight the bad microbes.

Microbiologists estimate an 85:15 percent ratio of good bugs to bad bugs is fine, but they aren’t sure. As one doctor explained microbial balance to me, “The good guys take up all the barstools so the bad guys can’t get a drink.”


Synergy is another one of the top concepts in healthy eating, and the reason why a multi-fruit smoothie or a multi-vegetable salad is so good for you. Synergy means, “We play better as a team.” Eat a variety of nutrients together—or, as Dr. Mom said, “Put more color on your plate”—so each nutrient prompts the others to do a better job for the body.

Could synergy be important for a healthy microbiome? Likely so. When you put many different kinds of good bacteria together (the term is “microbial diversity”), each one having a unique biological function in the gut, they team up better to keep the bad microbes in check.

The hormonal harmony of health is the theme of many of my health lectures. Your body is a symphony orchestra, and all the hormones, when they are in balance, play beautiful music. When they are out of sync, you get sick.

The same is true with your microbiome, which is why most of the bacteria in your bowels are called symbiotes, little bugs that play together for the health of their host.

The microbiome can significantly impact our health, making it a critical piece in your wellness journey! Gut health is a broad topic, but we hope this has given you a great starting point as you work to maximize your gut and brain health.

To learn more about improving your digestion, head over to Ask Dr. Sears!

Excerpt from Dr. Bill Sears’ T5 Wellness Plan; used with permission.