Sunday, November 16, 2014

We have met the enemy, and he is us.

Inside each and every one of us is a world so bizarre, so strange and alien that I couldn’t even begin to fabricate a story so seemingly impossible.

Inside of every person is an army that outnumbers every human that has ever lived on the face of the Earth—100 trillion strong, your intestinal microflora (hereon out known as ‘gut bugs’) is a living, breathing collection of hundreds of different species and families of invisible bacteria that control every facet of your being.  Your gut bugs are in your dreams, thoughts, and actions--they control your mind.  When properly cared for, your gut bugs are your best friends—when abused or neglected, they will turn on you.  Gut bugs can be your worst nightmare or the answer to all your prayers.

Why call them ‘gut bugs’?  They aren’t insects, they aren’t spiders or centipedes, so why do we call them bugs?  The term ‘stomach bug’ has been used for centuries to describe ailments of the intestines.  Got the flu?  Stomach bug!  Diarrhea, vomiting, or cramps?  Stomach bug!  We’ve known since the 1600’s that there are tiny, invisible microbes all around us.  During an 1850 cholera epidemic in London, the term ‘germ’ was coined as these bacteria were thought to be embryos of disease causing agents.  Later, all bacteria were thought to be germs and were often likened to disease carrying bugs.

People like to relate to things they can see—you cannot see microbes except with powerful magnification.  People don’t like the unknown, people want answers.  When talk of microbes surfaced in the early 1900’s, it was always in a bad way—who wants a stomach filled with tiny bugs?  Not me!  They’d say.  Anytime one had stomach problems, it was attributed to these ‘bugs’.     Bugs are something you can stomp on and they make such a pleasing sound when they crunch underfoot.  Infestations of bugs in a house are dealt with promptly by spraying them with a variety of easily obtainable chemicals or calling an exterminator when it gets completely out-of-hand.  Gut bugs are also just as easily dealt with—feeling under the weather, antibiotics will kill whatever nasty bug is making you sick.  Afraid of evil bugs in your food—boil the hell out of it, they will die.   

People like Louis Pasteur, Alexander Fleming, and Joseph Lister spent their entire professional careers attempting to destroy these bugs and developed antibiotics and sterilization procedures that have saved untold lives.  They also set into motion a series of events which changed mankind forever.

Everyone loves the term ‘gut bugs’.  It’s fun to say and conjures up images we can relate to.  There may be better terms, such as ‘intestinal microflora’, ‘intestinal microbiome’, or ‘gut microbiota’, but who wants to say those cumbersome words?  Everyone who deals with microorganisms of the intestines knows what gut bugs are, but hardly anyone knows what they really do.  Truth be told, this blog is really about more than gut bugs.  You will find out there are skin bugs, mouth bugs, and bugs on every surface of the body, but for now, we’ll stick to the gut bugs.  You will learn where these bugs come from, why we need them, and how to get rid of the ones that are in the wrong places.

Most gut bugs are living creatures made up of exactly one cell.  They are among the simplest forms of life and probably one of the earliest forms of life on Earth.  Gut bugs can be either spherical (called cocci) or rod-shaped (bacilli).  They all have cell walls which protect them from the environment.  A gut bug needs to eat, but it has no mouth.  It’s skin (cell wall) is rigid, but it can let molecules travel in and out.  Gut bugs have no nose, ears, or eyes either but they get around and communicate just fine.  Many of the bacilli (rod-shaped gut bugs) have tails they use to swim around in the fluids they live in.  Just like the lizards your cat likes to torment, these tails are detachable.  Some gut bugs have special tubes, known as pili, that they use to transfer material to other gut bugs.  What could a gut bug have that it needs to share?  Information!  When a gut bug detects an antibiotic, the first thing it does is share this information with its fellow gut bugs.  The smart ones will take this information and develop strategies to resist the antibiotics and become what the medical profession calls ‘super bugs’, gut bugs that can’t be killed by normal drugs.  In this sense, the term ‘computer bug’ makes a lot of sense.

Even though we think of microbes as simple cells, they are anything but simple.  Inside each microbe is a pool of water.  Inside this water lies a clump of bacterial DNA.  This DNA carries in it information that is millions of years old.  All of the functions of a gut bug are controlled by its DNA.  Everything the gut bug needs to survive is encoded in its DNA.  Also inside the gut bugs watery interior are ribosomes—these free-floating structures attach themselves to the DNA and carry out its instructions to make proteins, antibiotics, vitamins, poisons, and a complete line of every chemical imaginable.  Even more amazing, as science grows, so does our view of the microbe.  We have mapped the entire genomes of most gut bugs and even discovered cellular mechanisms that were unknown until recently.  Exosomes, noncoding RNA, microRNA, and even four-stranded DNA helices.  Gut bugs are anything but simple.

Everybody knows all about DNA, it’s that boring stuff that every living thing has inside its cells.  Big deal.  Well, microbes are even more complex than their DNA.  They  have obtained the ability to live in more environments than any other life form.  Known as "extremophiles," they are equally at home in boiling water and polar ice caps, they can live (and thrive) in oil spills, hot sulfur, salt, the air, dirt, and anywhere in between.  Some have developed gas pockets they can inflate at will to control their buoyancy in liquids.  Some microbes are magnetic and can navigate using the magnetic field of the Earth.  Some of these cells can transform into wall-less cells, or "cell-wall deficient" microbes and become even harder to detect and kill. All gut bugs share one common trait—they will do whatever it takes to get inside your gut, going to extremes that beggar the imagination to do so.

The human body is teeming with gut bugs.  Most of them are friendly and they do no harm.  Others can be deadly—meningitis, tetanus, cholera, pneumonia, and anthrax are all common gut bugs that thrive in, or outside, the human body and travel from person to person at will, often killing millions of people.  Again, the lengths at which gut bugs have evolved staggers the mind—corkscrew shaped gut bugs called spirochetes cause syphilis and Lyme disease.  Rickettsia is a gut bug that lives inside of other living cells and causes Lyme disease (not rickets).

But it's not all about the bacteria, either.  The fungal composition of our microbiome may be even more important than the bacteria and viruses.  Many even think the fungi that make up our "Myco-biome" are the true overlords of the human host, controlling the bacteria and even the host itself. Generally, when a person is weakened, the first pathogenic overgrowth seen is fungal. Invasive fungal infections are the biggest threat to critically ill Intensive Care Unit patients.  This fungi is driven through 4 billion years of evolutionary pressure to degrade dead or dying matter into a form that can be reabsorbed into the Earth.  But it can also keep us alive, and healthy, by fighting off bacterial, viral, and less friendly forms of fungi. 

 As mentioned earlier, people love to classify and label things.  This is especially evident when it comes to gut bugs.  You will see throughout this blog that gut bugs come in many flavors.  A very common way of identifying gut bugs is done through gram staining.

Hans Christian Gram was a Danish bacteriologist.  In 1884, Hans invented a way to classify our gut bugs into two large categories.  He found that he could collect microbes, stain them with special dyes, and if they turned purple he considered them 'Gram positive' and if they turned red they were 'Gram negative'.  This simple little discovery is, to this day, one of the most important tests done on gut bugs.

Gram staining is a very important lab test. It allows doctors to differentiate the two distinct bacterial groups.  This is critical in our modern world where a matter of minutes can be the difference between life and death.  Gram positive gut bugs respond well to certain types of antibiotics, like penicillin, while Gram negative gut bugs are very hard to kill and require harsher medicines.  Without this knowledge, it would take guesswork to treat patients and lives would be lost to time wasted in treating gut bugs that have ‘broken bad.’

Not only do people love to classify and name everything around them, it also seems we have a built-in need to count everything.  Ever try to count the stars, or grains of sand on a beach?  Well, counting gut bugs is just as hard—maybe even harder.  It is estimated that there are 500 to 1000 species of gut bugs living inside us.  There are ten times as many single-celled gut bugs as there are other cells in our bodies!  These numbers are staggering and incomprehensible to most, but let’s try to break it down and make sense of it all.

The number of cells it takes to make up a human (sans gut bugs) is 1013 .  Not many people realize what that number means.  It is written out like this: 100,000,000,000,000.  The number of people on the Earth right now is less than seven billion, 7X109, or 7,000,000,000.  The number of people who have ever lived on Earth is one hundred billion, 1010, or 100,000,000,000.  The number of gut bugs we possess at any given time is estimated at 1014, ten times the number of other body cells, 4000 times the number of people who have ever lived on Earth and  nearly 10,000 times the current population of the earth!  There are not many numbers of things bigger than the number of gut bugs we each possess.  For comparison, there are an estimated 1021 stars in the entire universe!

Most people aren’t impressed by big numbers with lots of zeros.  Just looking at our national debt, now $17,000,000,000,000, makes us give up on ever comprehending numbers that big.  Let’s put gut bugs in a different perspective:  If all the cells in your body were the same size as gut bugs, the cells that make up you would fit in one coffee can, but you’d need 10 coffee cans to store your gut bugs!  OK, enough on that—you get the picture…lots and lots of gut bugs.

Where do your gut bugs come from?  This question is still puzzling scientists.  When a baby is born, as soon as it the water breaks and it enters the real world, it begins to pick up gut bugs from everything it encounters.  Babies born via C-Section have completely different gut bugs than babies born naturally.  When breastfed, babies pick up gut bugs that live inside mother’s milk.  When bottle fed, a baby can lack certain gut bugs and may experience problems later in life.  Babies put everything in their mouth—coincidence?  Not by a long shot!  This is nature’s way of getting gut bugs into a human as quickly as possible.  Back in the day before running water and supermarkets, food was consumed covered in dirt and dirty hands ruled the day.  Many important gut bugs start their life cycle in the dirt and these soil-based organisms play a huge part in the chemistry of a thriving gut bug population.  As we age, our gut bugs change.  The gut bugs found in a baby are quite different from the gut bugs of an 80 year old—and with surprising consequences!

What do your gut bugs like to eat?  Another question that has only recently been tackled by scientists!  Turns out that gut bugs can eat almost anything you give them, and when there is no proper food for them, they eat you.  Different gut bugs eat different foods, some gut bugs eat only a part of a food item and other gut bugs eat the scraps—just like wild animals in a scene from a nature show.  But just as all gut bugs are not created equal—there are good ones and bad ones—gut bug food is not created equal, either.  It turns out that our good gut bugs like a very specific sort of food, and when they don’t get it, the bad gut bugs take over.

So, you still wonder, who cares about gut bugs?  What do they do for me other than make me sick?  Why don’t we just wipe them all out and live a peaceful life without all this drama?  As stated earlier, gut bugs can be your worst enemy or your best friend.  Gut bugs, good and bad, are associated with:

- Harvesting energy and nutrition from the food you eat
- Immune system
- Allergies, inflammatory bowel diseases, and overall body inflammation
- Obesity, weight loss and stability
- Cancer
- Metabolism
- Vaginal infections
- Recurrent urinary infections
- Diarrhea in adults and children
- Complications from antibiotic therapy
- Traveler’s diarrhea and/or colitis
- Lactose intolerance
- Hypertension
- Small bowel bacterial overgrowth
- Kidney stones
- Elevated blood cholesterol
- Flatulence
- Bacterial and fungal infections
- Rheumatoid arthritis
- Lupus and other autoimmune conditions
- Liver disease
- Autism
- Dyslexia
- Alzheimer’s
- Depression
- And more and more items are added every day!

The last question that most folks like to ask is, ‘Why all the bother?’.  If gut bugs are everywhere, and they are so versatile, why do we need to worry at all about them—can’t we just let nature take its course?  To some extent, we can.  In a perfect world, gut bugs would not even enter our thoughts—they should just be a working part of our body like our heart or liver.  But, like the heart and liver, we can cause damage to our gut bugs through poor lifestyle choices, uninformed eating habits, drug abuse, accidental or purposeful exposure to toxins, chemicals, pollution, and a whole host of other modern woes.  It’s time we take back our gut bugs and use what they’ve learned in their millions of years for our benefit.  This is all possible if you know your gut bugs and know yourself!  As Shakespeare said, ‘To thine own self be true!’


  1. Fascinating ... couple of typos though: commas have got in the wrong places in the written out 10 to the power of 13, and 7 billion is 7x10 to the power of 9, not 7 to the power of 9 (which is only about 40 million)

  2. you are developing a very flowing and easily readable style - keep up the good work.

  3. I think you're spot on about the reason why babies put everything in their mouths, and of course they crawl on the floor for months which must hugely increase exposure. They also scratch themselves lightly when babies and this may be another method of exposing microbes to the immune system. We all need to act like babies more.