The Zoo On You (Our Microbial Ecosystem)

Andrew Siegel, M.D.   Blog #77


There is an invisible “zoo” that lives on and in our skin, mouths, nasal passages, intestines, etc. We are literally teeming with this wildlife park of microscopic creatures —bacteria, viruses, fungi—that live on and in you and me. We are like coral reefs in the sense that other species take up harbor on or within us, although in this case, the tenants are microbial. This extensive menagerie of microorganisms consists of an incredible diversity of species with an estimated population of 100 trillion—collectively it is referred to as the microbiome.  Every one of us has a unique community of microbes, predicated on our genes, diet and environment.  This invisible ecosystem is dynamic and will change with variations in our diet and environment.

Many bacteria have been justifiably given a bad rap—methicillin-resistant Staph aureus (MRSA), E. Coli O157:H7, Clostridium difficile, etc.—as they are potentially very hostile creatures that can wreak havoc to our health and even kill us. However, not all bacteria and other microbes are our evil enemies; in fact, many are valuable, beneficial and are, in fact, vital for our health and existence, and that is the nature of our microbiome.

Our microbiome is primed at birth, when we depart the sterile environment of the womb.  Our initial exposure is to our mother’s vaginal flora or skin flora, depending upon whether the delivery is vaginal or via C-section.  This “jumpstarts” our immune system and provides us with our own micro-cosmos of creatures that will help us survive and thrive.  One of the key residents of a pregnant woman’s vagina is Lactobacillus.  This species usually resides in the gut, where it makes enzymes to help digest milk. During vaginal delivery, the baby is exposed to an abundance of these bacteria, theorized to prepare the baby to be able to digest breast milk.  Breast-feeding further charges up the microbiome, as breast milk contains hundreds of species of healthy bacteria.  In the first few years of life, our microbiome ecosystem gets increasingly complex as new microbes are added through contact with family members, our diet, and exposure to our environment including animals and other human beings.

There is a lot of truth in the following joke by George Carlin:

When I was a little boy in New York City in the 1940’s, we swam in the Hudson River. And it was filled with raw sewage! OK? We swam in raw sewage, you know, to cool off. And at that time the big fear was polio. Thousands of kids died from polio every year. But you know something? In my neighborhood no one ever got polio. No one! EVER! You know why? Cause WE SWAM IN RAW SEWAGE! It strengthened our immune system, the polio never had a prayer. We were tempered in raw shit!

Most of the invisible residents composing the microbiome are not harmful to humans and in fact, are vitally helpful to us in many ways.  This colony of aliens lives on our skin, in our nose, mouths, and gastro-intestinal and uro-genital tracts.  Our largest organ—the skin—is swarming with good bacteria, some of which break down the oily secretions of skin cells, creating a moisturizing film that provides suppleness and prevents cracks that could allow entry to those harmful microbes that can cause invasion and disease.

The greatest population of microbes resides in the gastro-intestinal tract.  This makes sense, since that’s where the most abundant food supply is.  Hey, why did Willie Sutton rob banks? …. Because that’s where the money is. We carry at minimum a few pounds of microbes in our intestines.  They confer many  advantages to us, including the following: they digest components of plant-based fiber that we cannot break down on our own; they synthesize vitamins, e.g, Bacteroides, which produces Vitamin K; they help release beneficial chemicals from food; they activate, train and maintain our immune systems; they suppress those microbes that can cause food poisoning, e.g., Lactobacillus salivarius in our mouths makes a toxin lethal to Listeria monocytogenes; and they guard against virulent (hostile) microbes by virtue of the magnitude of good bacteria present.

Our gut microbiome is very much influenced by our diet.  Interestingly, lean people seem to have very different intestinal microbes than obese people, and diabetics have very different intestinal microbes than non-diabetics.  Gut bacteria can digest fiber that we cannot on our own and are thus capable of allowing us to harvest additional energy.  The microbiome of obese people plays a role in regulating how cells use sugar for energy and in fat storage.  Certain bacteria in the gut can cause an inflammatory response that promotes fat storage and weight gain. It has been proposed that, like diet and exercise, gut microbes should be regarded as an additional factor affecting our overall energy balance.  Different gut microbiome composition can help explain why the absorption of nutrients and medications varies so much from person to person.

The fascinating story of Clostridium difficile (C. difficile)

This bacteria inhabits the intestine of about 8% of healthy people without causing harm or symptoms.  It remains non-hostile, as long as its population remains checked by the presence of a large population of healthy bacteria.  A C. difficile infection is commonly acquired under the circumstance of taking broad-spectrum antibiotics. These antibiotics not only kill the bacteria that they are intended to kill, but are also lethal to the “good” bacteria, allowing the C. difficile to flourish and predominate.  In the majority of people who don’t normally have C. dificile in their microbiome, it is acquired in hospitals or nursing homes, where it is spread by the fecal-oral route (not washing hands after bowel movements).  Toxins produced by the bacteria cause a horrible diarrhea with potential dire consequences.

In the United States, C. difficile causes more deaths per year than HIV infections.  The treatment of choice is to stop the broad-spectrum antibiotics that are responsible for killing off the good bacteria, and starting an antibiotic called Vancomycin, that is capable of killing C. difficile.  For refractory cases that do not respond to these means, fecal transplantation—transferring stool from a healthy donor to an ill patient to restore the normal balance of gut bacteria (i.e., the actual injection of healthy fecal matter into the colon via colonoscopy)—has proven highly effective.

How To Be On The Best Terms With Your “Zoo”:

  • Unless you have an immune deficiency, you do not need to live a life in quarantine—remember, in his joke, George Carlin made a very telling point.
  • Don’t use anti-bacterial soaps as they can kill off some of our good bacteria; good old plain soaps are just fine.
  • Don’t overdo it with hand sanitizers.
  • Don’t use antibiotic creams for every minor wound—clean with soap and water and cover with a band-aid.
  • Don’t beg your doctor for antibiotics.  More than 50% of antibiotic usage in the United States is both inappropriate and unnecessary.  Most common infections are viral—not bacterial—and the use of antibiotics is not only ineffective, but also a waste of resources and selects for a population of bacteria that are resistant to antibiotics.
  • Probiotics such as yogurt can help repopulate the microbiome if there is cause to believe it has been disturbed.  (This will be the subject of a blog in the very near future).

There’s no need to say “ewww” about your own personal “zoo”; rather, attempt to do everything to leave it undisturbed so that it can provide you with its natural health benefits.


Men’s Health, May 2012: The Dirty Little Secret Of Perfect Health by Jim Thornton

New York Times, March 20, 2012: Gut Infections Are Growing More Lethal by Denise Grady

Nutrition Action Newsletter, July/August 2012: Living In A Microbial World—Learning To Love Your Bacteria by David Shardt

New York Times, June 19, 2012: Attending The Bodies Microbial Garden by Carl Zimmer

ZOOBIQUITY: What Animals Can Teach Us About Health and the Science of Healing, Barbara Natterson-Horowitz, M.D. and Kathryn Bowers

Andrew Siegel, M.D.

Author of Promiscuous Eating: Understanding and Ending Our Self-Destructive Relationship with Food

Available in paperback or e-book on Amazon Kindle

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