Microbiome 101

What is the “microbiome,” and why should I care?

Mi·cro·bi·ome (mīkrōˈbīōm/)
the collective genomes of microorganisms (such as bacteria, fungi, and viruses) inhabiting a particular environment and especially the human body. Microbiota refers to the actual community of microorganisms, including their genomes.

Humans have multiple different microbial communities in and on our bodies. These dynamic communities inhabit our ears, eyes, mouth, gut, genitalia–just about any protected, resource-rich environment. In fact, some researchers urge us to think of our bodies as ecological “hosts,” because of the many microorganisms that that call us home. The genes in our microbiome actually outnumber the genes in our human genome by about 100 to 1! That means that by cell count alone, you are more microorganism than human.

You’ve come to the right place if you want to marvel at the incredible worlds within our bodies:

Evolution and our “old friends”

Humans and our microbiota have co-evolved throughout our evolutionary history—likely before we developed vertebrae! The bodies of our ancient ancestors offered protected and resource-rich habitats for these microbes, while the microbes began to perform important tasks. The “borrowing” of these microbial genes likely gave us a creative advantage, allowing us to develop new capabilities that we otherwise would not have. For example, microbial genes code for enzymes that break down food that we would not otherwise be able to digest. Others code for proteins that build nutrients, some synthesize vitamins, and still others produce molecules that keep harmful bacteria away. As these microorganisms began to take over certain tasks for us, our bodies were able to put energy into other capacities and possibly helped to make us the inventive species that we are today. While we’re only beginning to understand what these important microbes do for us, we do know that we wouldn’t be here without them.

What do our microbiota do for us

Gut microbes produce molecules that enter the bloodstream and travel around the body, affecting your metabolism. They influence how the liver and muscle cells store nutrients and use sugar. They signal our cells to store energy as fat or glycogen, regulating appetite and weight gain. They influence how your body responds to insulin, the hormone that regulates blood sugar. This means that the food we eat affects us directly, but also indirectly through our microbiota. So the next time you eat, think about how you are not only feeding yourself, but also your microbiota. Different diets support distinct communities of microbes, and the functions they perform will vary as such.

Extract nutrients
Microbes in our intestines break down foods that we can’t digest on our own. They are particularly prepared to digest carbohydrates, principally starches, fibers and sugars. These bacteria help us to release nutrients from our food that would otherwise pass through us undigested. This means that we get extra value for the food we eat.

Produce vitamins
Microbes in your large intestine synthesize vitamins that we don’t otherwise produce ourselves, including B vitamins. B vitamins are important for both human and bacterial cells in DNA synthesis and repair. They also take part in building amino acids and producing energy from fats and proteins—important and basic metabolic functions. B12, which can only be made by bacteria and archaea, helps build healthy blood and brain tissue. Some microbes synthesize vitamin K, which helps clot our blood, and supports the health of our teeth and bones. Other microbe-produced vitamins regulate blood sugar, strengthen the immune system, and keep the nervous system working properly. When we take good care of our microbial friends, we gain the benefit of their vitamin-producing genes.

Gut microbes train the immune system in a few different ways. These “good” bacteria stimulate the immune tissue around the gut, increasing the production of pathogen-fighting antibodies. Gut microbes teach the immune system to recognize and attack harmful invaders while leaving friendly species alone. The immune system learns to tolerate friendly bacteria, so that it doesn’t mistakenly attack our own cells (autoimmunity). Germ-free mice (mice that do not have a microbiome) don’t develop a complete immune system. The lymphatic tissue that normally grows around the intestine is disorganized and underdeveloped. The mice produce fewer antibodies, and they lack the complex capillary system that their microbe-filled counterparts develop early.

Moreover, certain bacteria in the gut release compounds that decrease inflammation. These compounds keep friendly microbes safe, by blocking attack from our immune system. These compounds also have a calming effect on us, preventing harmful inflammation and keeping the immune system from overreacting.

Protection from infection
Aside from supporting the immune system, friendly bacteria compete with harmful microbes, helping us (and them) to stay healthy. These communities of helpful microbiota produce a “biofilm” that blocks other more harmful organisms. These biofilms can develop on our skin and in our ears, eyes, nose, genitals, and gut. In order to colonize our bodies, new microbes must make their way through this protective shield to compete for resources and become part of the community.

Certain microbiota release molecules that keep competing bacteria and fungi away. In fact, more than half of the antibiotics used in medicine now are derived from compounds produced by the genus Streptomyces. The skin microbiota has a key role to play in this, as S. epidermidis bacteria signal our immune cells to produce a microbe fighting molecule that protects us from infection.

The healthy skin microbiome can also act as a barrier that keeps out harmful microbes. Microbes convert skin oils into natural moisturizers that keep skin soft, flexible, and crack-free. As bacteria break down skin oils, they also make byproducts that lower the skin’s pH. These acids keep undesirable bacteria from growing and penetrating our skin.

As bacteria in our gut break down carbohydrates, they produce a byproduct called n-Butyrate. This chemical is an energy source for our cells. It is also a signal that strengthens the connections between the cells of our intestinal lining. A strong barrier keeps food and harmful microbes from leaking through the intestinal wall into our bloodstream. Microbiota also promote healing of the gut. When the cells in our intestinal lining are damaged, bacteria release chemicals that signal nearby cells to start dividing, helping us heal faster.

Bifidobacteria keep toxins made by other bacteria (particularly lipopolysaccharides) from passing through the intestinal wall and into the bloodstream. Some microbes even inactivate toxic molecules that we ingest along with our food.

Brain, gut and other organ development
Microbes make two compounds (ARA and DHA) that signal brain cells to divide. These compounds have long been recognized as important nutrients, especially for babies and young children, whose brains are still developing. In fact, their apparent influence on learning and memory is so compelling that they are routinely added to baby formula in the attempt to mimic breast milk.

Recent evidence suggests that gut bacteria also send signals directly to the brain. The gut is surrounded by nervous tissue. Researchers increasingly refer to this collection of 500 million neurons as the “second brain.” Gut neurons connect to the brain, mainly through the vagus nerve, carrying information from the brain to the gut and from the gut to the brain. Interestingly, bacteria in the intestine make some of the same molecules that transmit signals in the brain: GABA, serotonin, melatonin, acetylcholine, and others.

Microbiota and disease

Here is a list of health conditions that are associated with a “dysbiotic,” or imbalanced gut microbiome:

  • Acne
  • Antibiotic-associated diarrhea
  • Asthma/allergies/eczema
  • Autism
  • Autoimmune diseases
  • Cancer
  • Chronic Fatigue Syndrome
  • Dental cavities
  • Depression and anxiety
  • Diabetes
  • Gastric ulcers
  • Hardening of the arteries
  • Inflammatory bowel diseases
  • Malnutrition
  • Obesity

Doctors have long viewed microbes as things to be gotten rid of. Viruses, after all, give us measles and the flu. Bacteria cause strep throat and food poisoning. But most microbes do not make us sick. And many are important for our health (see Your Microbial Friends).

As researchers learn more about the microbes that keep us healthy, we are coming to understand how subtle imbalances in our microbial populations can also cause disease—-and how restoring the balance may lead to cures. Our new understanding may lead to more focused and effective treatments. Unlike modern antibiotics, which kill good microbes along with the bad, new drugs may kill only harmful bacteria while leaving the friendly ones alone. Others may nurture friendly bacteria, helping them outcompete the harmful ones.

Symptoms of an imbalanced gut microbiome

Although many times an unbalanced gut microbiome will present itself through digestive issues, it can also show up in unlikely places:

  • Digestive issues common IBS, bloating, belching, constipation, diarrhea, heartburn, bad breath, abdominal pain, indigestion, acid reflux
  • Lactose intolerance
  • Chronic fatigue
  • Allergies and food sensitivities
  • Joint pain
  • Fibromyalgia
  • Chronic fungal and bacterial infections (systemic, urogenital, gut, etc)
  • Thrush
  • Depression, anxiety and mood disorders
  • Lowered libido
  • Low energy and chronic fatigue
  • Mental fog
  • Sugar cravings (including alcohol)
  • Unexplained weight gain and/or difficult weight loss
  • Skin problems such as acne, hives or eczema Skin conditions (acne, eczema, hives or psoriasis)
  • Hyperactivity; learning and behavioral disorders
  • Nail fungi
  • Autoimmune condition (such as Hashimoto’s thyroiditis, lupus or rheumatoid arthritis)
Causes of an imbalanced gut microbiome

Causes of an imbalanced gut microbiome can range from dietary, to lifestyle to geographical. This is why it is important to work with a qualified practitioner who can help you discover the root causes of your Dysbiosis such that your microbial community can re-balance and restore important functions. Causes include (but are not limited to):

  • Overseas travel (contaminated food and water)
  • Antibiotics
  • Overly sterile environments (over use of hand sanitizers, using bleach and household cleaners)
  • Use of NSAIDs: Abusing non-steroidal anti-inflammatory drugs (aspirin, advil, indomethacin, etc) inhibits growth of healthy bacteria and can cause leaky gut, which can cause a bacterial imbalance
  • Incomplete or Delayed Digestion
  • Toxicity (heavy metals, pesticides etc)
  • Changing hormone levels: Pregnancy, use of hormone elevating drugs, including birth control and steroid hormones, can all spark an imbalance of gut flora
  • Chronic stress
  • Diet: An overgrowth of fungus and yeast can be caused by a diet high in refined carbohydrates and sugar. Candida, a type of yeast, is the most common condition caused by a sugary and starchy diet. Candida lives off of sugar. This means any sugar you eat feeds it
  • Incomplete or Delayed Digestion (Chronic constipation from a digestive disorder, such as IBS, SIBO or leaky gut, will contribute to the imbalance of flora
What can you do for your microbiota?

Your gut microbiome is completely unique to you, as unique as your fingerprint. The specific proportion of which microorganisms inhabit your body are based on your life history and the decisions you make every day. This is why it is important to consult with a qualified practitioner who can sequence your microbiome to understand better what is going on and how to approach resolving the problems.

…Now that you understand why the microbiome is so important for health throughout our lives, let’s explore why the early development (in utero through the first years of life) are FUNDAMENTALLY important.