Until very recently, modern medicine’s war on microbes has been in full swing. Louis Pasteur proposed the Germ Theory of Disease in 1860. Armed with the knowledge that germs caused all disease, the Holy Grail of Medicine became to eradicate bugs: disease-causing bugs, bugs on our hands, bugs in our air, bugs in the soil and bugs in and ON our bodies. In the 1880s, an Austrian pediatrician began to theorize that there was a symbiosis between bugs and humans when he discovered E. coli in the intestines of healthy patients. However, it wasn’t until the 2000s that intensive study of the human microbiome began. The Human Microbiome Project conducted in 2007 opened up a whole new world of health, disease and the interrelatedness of life.
The Human Genome Project’s Surprising Discovery
On the tails of the Human Genome Project (HGP) in 2003, the Human Microbiome Project answered questions that left scientists stumped by the HGP. What baffled the HGP scientists was that the human only has 1.5 times the number of genes as a fruit fly and fewer genes than the flee. The assumption that the complexity of the human body would require hundreds of genes to function was shattered by the discovery that we are in fact LESS genetically complicated than a tiny bug.
What then makes us the complicated, intricate and miraculous beings that we are?
The answer is microbes. The discovery that the bacteria, fungi, parasites and viruses that inhabit every corner of our bodies and carry out tasks that genes would otherwise carry out is what made the Human Microbiome Project earth-shattering.
The HMP discovered that the human microbiome consists of up to 30,000 (according to Dr. Zach Bush MD) different species of microbes making their genomes outnumber ours by 100 times. The sheer number of microbes that live in and on us, however is not a astounding as the discovery of WHAT these microbes are DOING FOR US.
These microbes live a truly symbiotic life with ours. In our GI tract, they digest foods that would be otherwise indigestible to us, providing both us and them with nutrients, producing a multitude of vitamins, essential and non-essential amino acids, fatty acids and digestive enzymes. In fact, the microbiota do 90 percent of all the enzymatic work in the human body!!! NOT OUR ENZYMES, the MICROBES’ ENZYMES! They help to protect the epithelial lining of the gut as well as our immune systems from pathogens and toxins. They produce anti-microbial chemicals that help keep the “bad bugs” under control. When numbers are high enough, beneficial bacteria can suppress, out-compete and starve out pathogenic bugs in the body.
Immunity — Brought to You by Your Microbes!
The gut microbiome plays a crucial role in immune function and is the first line of communication between the immune system within the gut lining (the gut-associated lymph tissue, GALT) and the outside world. These microbes are in fact what educates and primes our immune systems in early life.
The development of a host’s immune system is affected by continuous and dynamic interactions with the intestinal microbiota and its metabolites. Bacteria are integral to the early development of the gut-mucosal immune system, both in terms of its physical components and its function, and continue to play a role later in life in its operation1
Allergies, Auto-immunity and …. You Guessed it: Our Microbes!
Exposure to intestinal bacteria is believed to prevent allergies and auto-immune diseases. Both conditions are an overreaction of the immune system to a molecule that should not pose a threat. The gut microbiome exposure early in life teaches the immune system what is “friend” and what is “foe.” Lack of this adequate exposure can lead to allergies, asthma, eczema, etc.
“Allergic infants and young children have been found to have a different composition of intestinal bacteria than those who do not develop allergies. It is hypothesized that the intestinal microbiota stimulates the immune system and trains it to respond proportionately to all antigens. An altered composition of intestinal microbiota in early life can lead to an inadequately trained immune system that can, and often does, overreact to antigens” 2
IBS, Irritable Bowel Disease and Our Microbes
Changes in the types and numbers of certain bacterial species have been associated with everything from IBS to ulcerative colitis and Crohn’s disease. The anti-inflammatory capabilities of good microbes are thought play a key role in the prevention and resolution of these diseases. In fact, inoculation with stool from healthy individuals has resulted in complete resolution of Ulcerative Colitis in as little as 1 week with complete remission in 4 months. 3
Obesity, Diabetes and Metabolic Disease
There is also a significant body of research evidence that points to the over-abundance of certain bacteria vs. another predisposing one to obesity and type 2 diabetes. Although the evidence of exactly which bacteria are responsible is not clear, it IS clear that dysbiosis (imbalance of species, lower numbers and less variety of species) plays a major role in these metabolic diseases. 4, 5
Eczema, Bored Teenagers and Healthy Bugs
Babies presenting with eczema in the early months of life were found to have lower bacterial diversity that infants without the skin condition. With regard to all allergies, the Hygiene Hypothesis proposes that the lack of exposure to microbes early in life leads to an overreaction to antigens because the immune system was never properly “educated” by exposure to microbes. Auto-immune disease is a similar overreaction of the immune system. One medical professional correlated the relationship between bugs and auto-immune disease this way:
“without having to deal with parasites, bacteria, and yeast, the immune system acts like a bored teenager: with nothing better to do, it reeks havoc on the system it inhabits.”
The moral of this example is that if we are not exposed to bugs, the system never gets the chance to identify “self” and “non-self.” This is the basic dysfunction that underlies both allergies and auto-immune disease.
Health=Diversity of the Microbiome
Dr. Zach Bush MD, who is a pioneer in the field of the the microbiome, talks about how certain parasites live in our eyelids and with out them the eyelid would become diseased. We know that microbes in our saliva protects our mouths from gum disease and cavities. We are also coming to realize that the most important thing that can happen to a newborn is to be exposed to his mothers vaginal flora. Dr. Bush’s most startling discovery has been that the diversity and populations of microbes DECREASES in CANCEROUS BREAST TISSUE, becoming a sterile environment at the later stages of cancer, while the healthy breast tissue is teeming with biodiversity. This, he postulates, indicates that a healthy, alkaline environment needs and supports a plethora of bugs while an acidic, cancer-ridden tissue no longer supports microbiotic life. In other words, health = a large bio-diversity of microbes living synergistically with us and able thrive and communicate. Disease = lack of biodiversity and a sterile environment.
What to Do to Fix the Situation
Over the past 10+ years, we have ALL become more and more aware that taking antibiotics can disrupt the beneficial microbiome. Physicians are just starting to consider the negative effects of handing out antibiotics like candy. Many are beginning to recommend that patients take a probiotic after the antibiotics to repopulate the essential microbiome.
However, in the real world, not enough is being done to preserve our valuable microbiome. 266 million prescription for antibiotics are still prescribed annually in the U.S., and although the probiotic industry is a multi-million dollar industry, our collective microbiome is 1/10 what it once was, both in diversity and in numbers. Many believe the skyrocketing rates of degenerative, neurologic and metabolic diseases we see today have their roots in this decimation of our microbes.
Unfortunately, we are getting EVEN MORE antibiotics from our food than we are from our doctors. Animals as well as crops are loaded with them. Round-Up, with its active ingredient glyphosate, is actually an antibiotic. Strayed on nearly every crop in the U.S., this chemical not only kills plants and pests, but kills all the microbes in everything it comes in contact with: the soil, the water, the air and our bodies. Unlike most toxins (which are fat soluble and stored safely away in fat), glyphosate is water soluble and has made its way into every nook and cranny of our environment. It is in our food, our water, our air and our rain.
Organic and Glyphosate-Free
If you are not eating organically, you must start now. Meat should be grass raised, not conventionally raised in a feed lot. Animals raised in feed lots are sick and need antibiotics. Staying away from factory-farmed animals removes the need for antibiotics in the animals. A wise choice is free-range, local farmer-grown. If this means eating less of it, then do that. We need to prevent antibiotic and glyphosate laden foods from being a part of our lives as much as we can control it. Since it is in our water, rain and air, we do not have 100% control, so do what you can, when you can. And GET ACTIVE! Ask your legislators to work toward stopping the use of glyphosate on all of our food!
(On a side note, another reason feed lots use antibiotics is because they cause the animals to gain weight faster. Hmmm. Doesn’t that make you wonder?)
Your Microbiome Needs Love
How do you feed your bugs?
- With organic veggies, because fiber is their food.
- With fermented foods to increase the number and biodiversity.
- By not killing them with chemicals and medications.
Taking probiotics can help, especially after a round of antibiotics, but according to Dr. Zach Bush, long-term use of a single probiotic (that contains from 3-12 strains) might just encourage “mono-cropping.” This is where we encourage the proliferation of just a few strains of bugs, instead of the thousands we need. Dr. Zach does think alternating between different Probiotic brands might help this.
Creating an Ecosystem
Dr. Bush believes that our microbiome SHOULD resemble a rain forest or coral reef. The diversity should be enormous. Eating WILD FERMENTS and feeding our bugs fiber WITHOUT glyphosate is a good start.
My favorite cure for a diminishing microbiome from Dr. Bush is:
“get out in nature and breathe. Breathe dirt, breathe air near a waterfall or ocean. Go hiking on a new trail. Pull weeds and you get a plume of bugs that explodes out of that dirt that you breathe in. The majority of our microbiome doesn’t come from our food but the air.”
Complexity and Symbiosis
I believe that the reason we have just a few thousand more genes than a fruit fly is because we were designed to live in harmony with bugs. That when we disconnect from nature and the trillions of microbes in it, we start to get sick.
Love your bugs because they are literally keeping us alive!
If you would like more information about how to incorporate microbiome-friendly foods into your diet, would like a health consult or any other dietary, lifestyle or supplement support from Dr. Katania, you can contact her at firstname.lastname@example.org. Visit me! And check out my Oral Health and Kid’s Transformational Health Programs.