Life in and on Us.

On my rounds with the interns and residents, I stumbled across a stocky woman who was quite ill with raging diarrhea. Her name was Melanie, and she was running a fever and had abdominal pains that felt like she was being punched in the gut every 5 minutes.  A burst of watery diarrhea would follow that.  She was ill and had suffered these indignities for days. She had been on antibiotics for a urinary tract infection for some weeks and developed this bowel problem only recently.  Melanie was suffering from a severe illness—a deadly one—caused by a bacterium Clostridium difficile that takes advantage of a bowel in which most of the normal flora have been killed by antibiotics.  It is a common problem and one which is quite severe. The crazy thing about C. diff, as it’s called, is that we use other antibiotics to kill those bugs and, in some ways, fight fire with fire.  Melanie was in dire straits and could die on us.  She had this bug intermittently for the past several months and was weakened by diarrhea and running out of steam because of this chronic infection. With very few options, we elected to transplant stool into Melanie’s bowel through her rectum in a procedure called a colonoscopy.  The stool from a patient with normal flora was given to her in capsule form. We were attempting to seed her bowel with organisms from someone else.  We were moving a normal biome from someone else into her with high hopes that her symptoms would go away, and she would live an everyday life. Stool transplants have a cure rate of 90%.

For those of you like Howard Hughes who believe that everything is covered with a small layer of dirt and behave as though your neighbor is giving you illness because of their unkempt lives, that all food is spoiled and contaminated, you need to read on. If your child is eating dirt, playing in the cat box, or wrestling with your dog, you should take comfort that he might adjust his adaptive immune system to respond to horrid infections later in life.  Biomes are communities of organisms within and on us.  When I was a youngster, I read a book entitled “Life on Man,” a book of interest to college students smitten by biology that foreshadowed my interest in all the organisms in our surroundings that become a part of our bodies.  There are trillions of bacteria in our bowels, hundreds of millions on our skin, and likely many more within our lungs, mouth, and urogenital tract. In the gut alone, there are roughly 100 trillion microorganisms. The number of genes resulting from these organisms in the bowel is 150 times greater than our genome.  Biomes are present everywhere in the body.  Most notably, the female vagina and male reproductive tracts have biomes as well—and that has particular importance. These communities of organisms are vital to our well-being, the health of the immune system, which it informs from and even before birth, and our mental and physical well-being. Our mental well-being can depend on organisms that thrive within us, essentially your soul mates whose names you cannot pronounce and whose microscopic forms are probably enough to scare you.  This is how the environment affects you in a big way, and you might have second thoughts about certain aspects of your diet and your behavior after digesting some of these facts.  Data show that you are “what you eat,” we used to joke about that when it came to obesity, but it’s no longer a joke but a fact of life.  You can take comfort in the fact that you carry whole communities of organisms around you that are processed by your immune system and constantly identified as friends or foes.

I mention that the microbiome acts as an adjuvant for vaccines, meaning that your response to a vaccine will be affected in part by the flora of your bowel. An adjuvant is an assist to any vaccine injected into you. When germ-free mice are born without exposure to organisms—essentially sterile and fed sterile diets- they fail to mount an immune response to the influenza virus.  A similar response was found in the mice that were given massive doses of antibiotics and had their bowels chemically sterilized.  Most vaccines contain materials like aluminum to prod the immune response, and these organisms are the endogenous or inner nudge from the bugs in your bowel.