It’s time to get this thing done. It stands currently at 19 Chapters and two substantial appendices. This is Chapter 1, and I will publish Chapter 2 here (Your Second Brain), within a few days to a week, when it feels right.
And it now feels like the right and prime time to drive it home. Timing and circumstances continually plagued me since Tim “Tatertot” Steele and I set out to do this. Over and over, I thought I was on the cusp of diving in and getting it done, only to have a crazy gonzo life get in the way. I’ll not bore you with details. It’s just furiously onward, now.
I present chapter one…
Who are you? A doctor? A farmer? A father, mother, son, daughter? You may be any of these or a few, but it isn’t even close to describing who you really are in total. You aren’t even a single entity, but a collection of living things that work in unison, mostly symbiotically. Inside each and every one of us is a world so bizarre, so strange and alien, that we couldn’t even begin to fabricate a story so implausible. It’s science, not fiction—and the unison of the two is ironically less strange.
To make sense of it, we often call it nature, a sort of catch-all. Or, we punt in various ways, invoking superstition. Doing so is probably nature and natural, too.
LET’S JUST SAY LOTS AND LOTS
There’s about 40 million bacterial cells in a gram of soil and about a million bacterial cells in a milliliter of fresh water. In total, there’s estimated to be about five million trillion trillion, or 5 × 1030 (5 nonillion) bacteria on Earth with a total biomass equaling that of plants. Some researchers believe that the total biomass of bacteria exceeds that of all plants and animals.
Inside of every human organism are armies of microorganisms with DNA that are entirely different from our human cells. That microbiome not only outnumbers your human cells by a factor of ten to one but in total, it outnumbers every individual human that has ever lived on Earth. Your intestinal microflora numbers 100 trillion! Compare that with the total estimated 110 billion humans who have ever been born. You’ve got 900 times as many microorganisms as that. Your internal “civilization” of ‘gut bugs’ is comprised of up to 1,000 different species with 3 million non-human genes, compared to your own 24,000.
But, perhaps large numbers aren’t your thing. After all, the U.S. National Debt now stands at over $17,000,000,000,000.00, and that doesn’t appear to alarm too many; and many seek to double it, in order to get their favorite microorganism into some quorum-sensing position we call elected office. Perhaps the numbers are just too big to comprehend. So let’s look at it another way. Suppose all of your human tissue cells (organs, blood, bone, etc.) were the same size as your bacteria. They would all fit in one coffee can. However, you would need 10 cans to store your bacteria. And did you realize that approximately 60% of your stool is made up of the dead ones? So, yea: lots and lots.
EVERY BREATH YOU TAKE AND EVERY MOVE YOU MAKE
Our gut microbiome is a living, breathing—and especially: eating, metabolizing, secreting—colony of these some hundreds of different species and families of invisible bacteria that, in myriad ways, influence all facets of your being. Your gut bugs are in your dreams, thoughts, and actions. They even influence your mind to the extent that an NPR piece in November, 2013, suggested that “Gut Bacteria Might Guide The Workings Of Our Minds.”
“I’m always by profession a skeptic,” says Dr. Emeran Mayer, a professor of medicine and psychiatry at the University of California, Los Angeles. “But I do believe that our gut microbes affect what goes on in our brains.”
Mayer thinks the bacteria in our digestive systems may help mold brain structure as we’re growing up, and possibly influence our moods, behavior and feelings when we’re adults. “It opens up a completely new way of looking at brain function and health and disease,” he says.
So Mayer is working on just that, doing MRI scans to look at the brains of thousands of volunteers and then comparing brain structure to the types of bacteria in their guts. He thinks he already has the first clues of a connection, from an analysis of about 60 volunteers.
When properly cared for (e.g., fed, and fed properly), our gut bugs can be our best friends. But, when abused or neglected, they can turn on us or, the balance where the many good species keep the bad ones in check is tipped, in favor of the bad ones. With that in mind, consider this second excerpt from that NPR article.
Scientists also have been working on a really obvious question — how the gut microbes could talk to the brain.
A big nerve known as the vagus nerve, which runs all the way from the brain to the abdomen, was a prime suspect. And when researchers in Ireland cut the vagus nerve in mice, they no longer saw the brain respond to changes in the gut.
“The vagus nerve is the highway of communication between what’s going on in the gut and what’s going on in the brain,” says John Cryan of the University College Cork in Ireland, who has collaborated with Collins.
Gut microbes may also communicate with the brain in other ways, scientists say, by modulating the immune system or by producing their own versions of neurotransmitters.
“I’m actually seeing new neurochemicals that have not been described before being produced by certain bacteria,” says Mark Lyte of the Texas Tech University Health Sciences Center in Abilene, who studies how microbes affect the endocrine system. “These bacteria are, in effect, mind-altering microorganisms.”
It’s worth entertaining the possibility that many individual and societal health problems have their root cause in how our guts are being fed improper foods, neglected, or even abused.
THE ONLY GOOD BUG IS A DEAD BUG
…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 comfortable answers and certainty. When talk of microbes surfaced in the early 1900’s, it was always in a bad context—who wants a stomach filled with tiny bugs? “Not me!” Anytime someone had stomach problems, it was attributed to “bugs.” Bugs are something you can stomp on and they make such a pleasing sound when they crunch underfoot, and so they served up a fitting metaphor in the spirit of comfort and certainty.
Infestations of bugs in a house are dealt with promptly, by spraying them with easily obtainable chemicals, setting traps, or calling an exterminator when things get completely out-of-hand. And yet, modern science has demonstrated over and over again that in nature, there is a place—a crucial role—for all of the bugs—typically as some form of predator and then, prey. Simply stated, they are an essential link in the food chain in the various environments they inhabit. So what’s the disconnect? It might “bug” you to consider it, but they’ve been around a lot longer than we have, and they didn’t evolve in an environment of urban centers and fixed human dwellings, nor amongst beds with mattresses and pillows.
But the comforting bug metaphor has long since been operative in how we humans generally approach the bacteria in and on us. It’s understandable because after all, our awareness was only raised by the bad ones…the pathogenic, the communicable, the maimers and killers. It was an easy precaution to take: the only good bug is a dead bug. So the bacteria inhabiting humans were dealt with the same way as the bugs invading your home or your bed. It’s unjust to implicate life-saving advances in medical science that at first, discovered simple sanitary practices like hand washing, cleaning, doing the laundry, proper disposal of refuse, disposition of the dead, and then later went on to develop antibiotic agents and medicines to combat infections. Hundreds of millions of human lives have been saved by such advances in knowledge and intervention.
NOT SO FAST!
So what’s the disconnect? It’s that, unlike those bad-bug infestations, the vast majority of “bugs” in your body are not infestations, but rather, essential to your health and well being. They belong there. They’ve been with us from the start. And for as many lives as have been saved by the use of antibiotics, they are but a blunt instrument that not only kills the pathogenic bacteria, but the symbiotic and beneficial as well. Moreover, an important function of all the good microbes is that they tend to keep the bad ones in check. For example, you may have heard of the spore-forming bacteria, Clostridium difficile, or C. diff, that in America alone, sickens a half million annually, hospitalizes 250,000, and kills 14,000. What you may not be aware of is that many normal people have the C. diff bacteria in their gut already. It’s kept in check by the good guys. Kill too many good bugs? Guess. According to the Mayo Clinic:
Your intestines contain millions of bacteria, many of which help protect your body from infection. But when you take an antibiotic to treat an infection, the drug can destroy some of the normal, helpful bacteria as well as the bacteria causing the illness. Without enough healthy bacteria, C. difficile can quickly grow out of control.
Pioneers in medicine like Louis Pasteur, Alexander Fleming, and Joseph Lister spent their entire professional careers developing the means to prevent, combat, and eradicate known, obvious pathogens. They achieved wonders and saved millions of lives. But we now know what they couldn’t have understood in the context of their time. They never understood the delicate balance that exists within us, in our guts, and all around us. Unwittingly, perhaps unavoidably, they set in motion a series of events that changed mankind forever.
For better or worse, we’re going to be stuck with the term gut bugs. It’s amusing to say, and conjures metaphorical images we can relate to. But just as we’ve come to understand that the real bugs in nature have important roles to fulfill, and everything is fine when nature’s elegant balance is in play, so we can also come to understand that the same holds true for the “bugs” in our gut.
TOWARD AN EMERGING UNDERSTANDING
With that out of the way, we can move on to a better understanding of precisely what roles these many species play in terms of our health and well being. And here’s another surprise: there’s more than just microbes in your gut. You’ll find that there are skin and hair bugs, mouth bugs, nasal bugs, vaginal bugs, reproductive tract bugs, and more. While our primary focus will be on the gut—our second brian—we’ll touch on all of these in forthcoming chapters. You’ll want to know where these bugs come from, why we need them, what most do that benefit us, and what the few do that harm us.
And wouldn’t you like to know how to naturally control or eradicate those pathogens too numerous, or in the wrong places? We’ll focus on that as well.
BACTERIA ARE AWESOME
Bacteria are living creatures made up of exactly one cell. They’re amongst the simplest forms of life—probably one of the earliest forms of life on Earth. Our personal microbes are mainly either spherical (called cocci) or rod-shaped (bacilli). They all have cell walls that protect them from the surrounding environment. Bacteria require nourishment, but have no mouth. Its skin (cell wall) is rigid, but it can allow molecules to travel in and out. They have no nose, ears, eyes, arms, or legs; but they’re mobile, and they communicate. Many of the bacilli have tails, used to navigate the fluids in which they inhabit. As with the lizard, their tails are detachable. Some have special tubes, known as pili—used to transfer material to other microbes. But what could a single-celled organism have that it needs to share? Information! For instance, when an antibiotic (a poison to the organism) is detected, this information is shared with its fellows. Over many lifecycle generations, bacteria evolve to resist antibiotics and become what the medical profession calls superbugs—bacteria that can’t be eradicated by the antibiotics du jour.
Even though we know bacteria to be single cells, they’re anything but simple. Within the cellular membrane of each is contained mostly water. Within this water resides the material of DNA. DNA carries genetic information that’s literally billions of years old, and all cellular functions are controlled by it. That’s right: our microbiome is operating, in part, on basic instructions billions of years older than primate life itself! If that’s not impressive enough—recalling that our gut microbes possess a combined 3 million genes to the 24,000 for our human cells—also present in this watery interior are ribosomes. These free-floating structures attach themselves to DNA to carry out instructions to manufacture proteins, antibiotics, vitamins, hormones, poisons…a veritable complete line of synthesized chemicals. Our microbes, each of some 100 trillion, are only single cells that are, nonetheless, microscopic chemical plants, the likes of which ought to make Eleuthère Irénée du Pont, Herbert Henry Dow, and Friedrich Engelhorn all blush.
Microbes are astoundingly complex, versatile, and resilient, even though a single complete microbial life might be measured in mere minutes. Various strains have obtained the ability to live in a wider array of environments than any other life form. They can be equally at home in boiling water, and polar ice caps. They can live and thrive in oil spills, hot sulfur, salt water, the air, dirt, and everywhere in between. Some have evolved ballasts to control buoyancy in liquids. Some microbes are magnetic, navigating by means of the Earth’s magnetic field. In terms of our gut microbiota, they all have one thing in common: whatever it takes to get inside your gut, as that’s where its kind took up residence millions of years ago in the first primates.
Since they’re quite effective getting where they belong, in a protected environment with a constant supply of nourishment, our bodies are teeming with them. The vast majority are mutualistic. But a few can be deadly—meningitis, tetanus, cholera, pneumonia, and anthrax are all common bacteria that thrive in, on, or outside the human body, potentially infecting and killing millions. The lengths to which bacteria have evolved to do good or harm in all facets of life is staggering. …Corkscrew shaped microbes called spirochetes cause syphilis and Lyme disease. …Rickettsia is a pathogen that can only live inside of other living cells, causing typhus and Rocky Mountain spotted fever. Other bacteria,—such as the much maligned e. coli, the culprit behind many food-poisoning outbreaks—are only harmful when found in large numbers or where they don’t belong; but when living happily in your gut are crucial to keeping other pathogens at bay. Conversely, there are gut bugs that appear to do nothing but good things for us…bifidobacteria is one type of microbe with no downside—their presence is linked with excellent immune function and vigorous health.
Hans Christian Gram was a Danish bacteriologist who, in 1884, invented a way to classify bacteria into two large categories. He found that he could stain bacteria with special dyes and if they turned purple, they were considered ‘positive’; but, if they turned red, ‘negative’. Later, these classifications became Gram positive and Gram negative. To this day, Gram staining is one of the most important tests done on bacteria.
Gram staining allows medical professionals and lab technicians to differentiate between two distinct bacterial groups—critical in a medical emergency where minutes count. Gram positive bacteria respond well to certain types of antibiotics, like penicillin, while Gram negative bacteria are very hard to kill and require harsher drugs. Without this knowledge, it would take much more guesswork to treat patients, with lives lost to time wasted.
There are dozens of other ways in which bacteria have been classified over the past 50 years, with new methods being developed all the time.
HOW DID THEY GET THERE?
Where do your gut bugs come from? From 1900 until very recently, it’s been held as dogma that human infants are born with sterile guts, and only begin acquiring microbes during the trip down the birth canal and subsequently, through breastfeeding and human contact. However, we now that’s not the case (even though you still encounter the myth frequently) and fetuses are seeded with gut bacteria while still in the womb. When breastfed, infants subsequently pick up hundreds of bacterial strains in mother’s milk, as well as oligosaccharides that constitute food for the bacteria. This combination of prebiotics and probiotics results in a rapid structuring of the newborn’s gut to favor almost exclusively probiotic strains of bifidobacteria and lactic acid bacteria. Subsequently, the newborn touches everything it can gets its hands on, including the skin, mouth, hair, ears, and faces of other humans it encounters. And it puts its fingers in its mouth all the time! The infant enters the real world and begins to pick up and seed its gut with bacteria from everything it encounters.
Babies born via C-Section and/or have been formula fed have fewer beneficial strains of gut microbes than those born and fed naturally. Lacking certain gut bacteria can lead to problems later in life, particularly in terms of allergies and asthma, already associated with C-Section and formula feeding. Add to all of this the modern obsession with sanitation and cleanliness. The only good bug is a dead bug, remember? But back in the days 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 large part in the biome population of a thriving gut. 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.
Green Iguanas (Iguana iguana) undergo a three-step process to acquire gut microbes before they begin eating normally. For the first week after hatching, they eat nothing but dirt from the nest chamber. Then during their second week of life, they eat both plants and soil from around the vicinity of the nest site, and finally at 3 weeks of age they leave the area and eat the feces of older iguanas before embarking on a life of foraging for plants.
FEED YOUR GUT
What do your gut bugs like to eat? It’s a question that has only recently been the focus of nutrition science inquiry. Turns out that they can eat almost anything you give them; and when there is no proper food for them, they eat you. Different bacterial strains eat different foods, some eat only part of a food item, and others scavenge the scraps—just like wild animals in a scene from Animal Planet. But just as gut bacteria are not all created equal—there are good ones and bad ones—their food is not created equal, either. It turns out that our health promoting bacteria like very specific sorts of food, and when they don’t get it, the bad bugs take over.
WE’VE MET THE ENEMY AND IT’S US!
Who cares about gut bugs, and why should we? What do they do for us, other than make us sick? Why not just wipe them all out and live a peaceful life without all the drama? Well, first, it would be impossible. Unless you live in a sterile environment, bacteria will just get right back inside you and take up residence in your gut once again. You’re stuck with them, so you might as well learn a little about them—especially your health promoting allies, because they’re your chief defense against your enemies. The microorganisms living in your gut can be your worst enemy or your best friend, and both the goods ones and bad ones are associated with all of the following, which should be viewed from both ends of the spectrum; i.e., good function or prevention vs. bad function, or onset of an adverse condition:
- Harvesting energy and from the food you eat
- Vitamin and mineral absorption
- Vitamin synthesis (yes, some bacteria synthesize essential vitamins)
- Immune system function
- Allergies, inflammatory bowel diseases, and systemic inflammation
- Obesity, weight loss and stability
- Vaginal infection
- Recurrent urinary tract infection
- Diarrhea in adults and children
- Complications from antibiotic therapy
- Traveler’s diarrhea and/or colitis
- Lactose intolerance
- Small bowel bacterial overgrowth (SIBO)
- Kidney stones
- Elevated blood cholesterol
- Bacterial and fungal infections
- Rheumatoid arthritis
- Lupus and other autoimmune conditions
- Liver disease
With more associated conditions being discovered all the time.
The last question folks will often ask is, “why all the bother”? “If gut bugs are everywhere, and they’re so versatile, why do we need to worry about them at all—can’t we just let nature take its course?” To some extent, we can. In a perfect world, our gut flora would never even enter our thoughts—and they’d be just a working part of our body like a heart or a liver. But just as we can do damage to our various organs through action or neglect, so can we do damage to our guts 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 understand their incredible complexity just a little and learn to use what they’ve learned in their billions of years that’s potentially for our benefit. This is all possible if you know just a little bit about the other part of you, and it’s our job to reveal that to you throughout this book.
Shakespeare said “To thine own self be true,” but as you know by now, your own self isn’t all of you.
 “Biomass (ecology) – Wikipedia, the free encyclopedia.” 2006. 9 Feb. 2014 <http://en.wikipedia.org/wiki/Biomass_(ecology)>
 Spore forming means that the bacteria has a means of laying dormant for extended periods in extreme heat, cold, or dry, and then, when conditions are right, germinate just like the seed of a plant.
 Mankind’s fate was already sealed as soon as he moved from the jungles, plains, mountains and seashores into villages and built structures, lived in dense proximity one to another, piled up refuse, drank from contaminated water supplies and all manner of things that made a breeding ground as well as an effective means of transmission for pathogens.
 The life of most bacteria is counted in minutes to a few hours, depending on the particular strain. Thus, natural selection over many generations can happen quite rapidly.
 A minute particle consisting of RNA and associated proteins, found in large numbers in the cytoplasm of living cells. They bind messenger RNA and transfer RNA to synthesize polypeptides and proteins.
 “Mom Knows Best: The Universality of Maternal Microbial Transmission.” 2013. 9 Feb. 2014 <http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001631>
 Human Milk Oligosaccharides (HMOS). HMOS have a unique cell structure in that they display ligand mimicry. Pathogenic microbes—and most non-pathogens—will attach themselves to these HMOS and not the epithelial cells of the small intestine. This prevents small bowel infections, diarrhea, etc., and is one reason newborns are so relatively bulletproof. Moreover, all HMOS aren’t digested by bacteria; some enter the blood and urine streams where they further scrub pathogens from the infant.
 Azad, MB. “Gut microbiota of healthy Canadian infants: profiles by mode of …” 2013. <http://www.cmaj.ca/content/185/5/385>
 Montiel-Castro, AJ. “The microbiota-gut-brain axis: neurobehavioral correlates, health …” 2013. <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791857/>