What is the Microbiome?

Our brain, gut, immune, and hormonal systems are intricately interconnected—and recent research has brought many fascinating studies about how crucial our microflora is to our bodies. These microorganisms are now understood to be crucial to genetic expression, body weight, mental health, memory, and risk of diseases as varied as Crohn’s, IBD, obesity, to diabetes and cancer.

The human body functions largely due to the presence of microorganisms including bacteria, fungi, and viruses. It is estimated that approximately 90% of the cells in and on the human body are those of microorganisms, and only 10% are actually human cells. Though there are microorganisms living on virtually every surface of the body, there are a few areas of interest that are generally referred to when one speaks of the microbiome. These are:

  • Gastrointestinal tract. This is the most commonly talked about area of the microbiome, largely to its diverse and vast population of microorganisms, and its wide-reaching effects on the body. According to the European Society of Neurogastroenterology and Motility, the gut microbiota includes tens of trillions of microorganisms, including over 1000 different species of bacteria, and can weigh up to 4.5 pounds. The gut microbiome aids the body in food digestion and nutrient absorption, and also plays an important part in immune functioning.
  • Mouth. Like the gut, the mouth has a large population of microorganisms. According to a recent study published in the American Society for Microbiology, the mouth is estimated to house anywhere from 500-700 species of bacteria. The same study also reports that the mouth microbiome composition may also be responsible for oral infectious diseases (tooth decay, gum disease, etc.) as well as systemic diseases such as cardiovascular disease, stroke, preterm birth, diabetes, and pneumonia. [NOTE: hyperlink to all relevant condition centers]
  • Skin. The skin is the body’s largest organ, accounting for approximately 15% of the average human’s body weight. The skin is host to a multitude of microorganisms that assist it in its many functions, including sweating, heat and fluid retention, and acting as an immune barrier. The constitution of the skin microbiome is largely dependent on the skin surface, the individual’s health, and the external conditions. Because of the variety of factors affecting the skin microbiome, these microorganismal populations tend to be extremely unique. A 2013 study published in Natural Reviews Microbiology found that an average of 68.1% of the bacteria found on a subject’s skin was only found on that particular subject.
  • Vagina. The vagina is populated by trillions of microorganisms that change throughout a woman’s lifetime. Potential factors affecting vaginal microbiome include menstruation, sexual intercourse, douching, and pregnancy. According to the vaginal microbiome consortium, a healthy vaginal microbiome can help prevent sexually transmitted infections, urinary tract infections, and bacterial vaginosis as well as help promote healthy pregnancy.

There is still much ongoing research into the human microbiome; the full effect of the microbiome constitution on human health is not yet known.

What Causes an Imbalanced Microbiome?

A healthy microbiome has a diverse population of microorganisms with no one population outgrowing the others. There are many factors that can cause disruptions to a healthy microbiome. These include:

  • Stress. Stress affects the level of stress hormones within the body and can make an individual more susceptible to changes in his or her microbiome.
  • Diet. The connection between diet and microbiome is one of the most highly contested and controversial areas of microbiome research. Many insist that relatively recent shift to high-fat and high sugar foods has caused shifts in the microbiome that have made the modern human more susceptible to diseases such as cancer, diabetes, inflammatory bowel disease, and obesity. Other controversial dietary items include meat raised with antibiotics and genetically modified organisms (GMOs).
  • Disease. Certain conditions, such as irritable bowel syndrome (IBS) and Crohn’s disease are thought to affect microbiome constitution. It is not known for certain if a disruption to the microbiome is a cause or effect of these conditions.
  • Antibiotic usage. It can take the body up to six months to return to a healthy microbiome state after a single round of antibiotics. Though antibiotics can be critical in treating a patient with a bacterial infection, there is fear that the over-prescription of antibiotics (and the lack of complimentary probiotic treatment) can lead to imbalances in the microbiome responsible for health problems such as obesity and chronic illness.
  • Environment. Humans are always engaging with the microorganisms in their environment; microorganisms cover nearly every surface we touch. The microorganisms in one’s home environment are likely to be found within that person’s healthy flora. Interacting with microorganisms from unfamiliar environments (i.e. while travelling) can have potentially disruptive effects on the health and microbiome (i.e. diarrhea, bacterial infection, etc.)
  • Family history. While microbial communities vary greatly between different households, they are similar amongst members of the same household according to research published in Science—and certain microbiota imbalances may carry throughout.

What is the Function of the Microbiome?

Researchers have already identified many possible functions of the microbiome. The functions of the microbiome can vary from location to location, though it is important to note that the microorganismal populations in these areas can and do interact with each other.

The known functions of the microbiome according to location are as follows:


  • Immune functioning. The microorganisms lining the gut form a barrier that can prevent potentially harmful bacterial populations from colonizing.
  • Production of vitamins. Microorganisms within the gut can help in the production of B and K vitamins.
  • Aids digestion of otherwise indigestible foods such as cellulose (found in plant cell walls).


  • Immune functioning. The microorganisms within the mouth play an important role as a barrier from potentially harmful microorganismal populations. This can protect against systemic illnesses and those specific to the mouth (tooth decay, gum disease, etc.)


  • Immune functioning. Like the other microbiome locations, the skin and the microorganisms on it function as an important barrier for the body against disease.
  • Health/appearance of skin. The appearance/health of skin is largely influenced by the microbiome population of the skin. The skin microbiome constitution can contribute to conditions such as dry skin, oily skin, acne, and various skin rashes.


  • Immune functioning. The vaginal microbiome can help protect against diseases such as:
    • Bacterial Vaginosis (BV)
    • Sexually transmitted infections
    • Urinary tract infections (UTIs)
    • Yeast infections
    • A healthy microbiome promotes fertility as well as decreases the risk of pregnancy complications.
    • A fetus does not have a microbiome until birth. According to the Vaginal Microbiome Consortium, a mother’s vaginal microbiome plays a critical role in establishing her baby’s microbiome during its passage through the birth canal. Babies that are born via cesarean section do not pass through the birth canal and instead begin populating their microbiome once they are removed from the womb.

Microbiome at Birth

The building of a microbiome begins at birth. Fetuses are sterile in the womb, meaning they do not house any microorganism populations. As they pass through the birth canal, they are introduced to organisms from their mother’s vaginal microbiome and start to build their own microbiome. Babies that are birthed via cesarean section begin building their microbiome with skin microorganisms. Even the environment into which the baby is born (i.e. hospital, home) has an effect on the formation of its microbiome. It has been suggested that babies born vaginally have a more robust immune system even into adulthood. The full effects of the differences between home and hospital, skin and vaginal microbiomes are not yet known.

The microbiome experiences its most rapid growth and expansion during infancy and childhood. The environment in which the child is raised as well as the food they are fed will affect the composition of the microbiome.

Symptoms of Imbalance in Your Microbiome

There are many different symptoms that could mean an imbalance in the microbiome. Because most of the symptoms of an unbalanced microbiome could also be signs of other potentially serious conditions, it is important that you contact your doctor to determine the cause of your symptoms.

The following could be signs of an unbalanced microbiome:

  • Acne
  • Asthma
  • Athlete’s foot/fungal infections of the skin
  • Body odor
  • Brain fog
  • Bloating
  • Chronic fatigue
  • Decreased sex drive
  • Excessive flatulence
  • Flu-like symptoms
  • Frequent colds/flus/infections
  • Headache
  • Hemorrhoids
  • Hives/frequent skin rashes
  • Indigestion
  • Insomnia
  • Intense cravings for sweets and sugary drinks (soda/alcohol)
  • Irregular menstrual cycle
  • Memory loss
  • Mucus in stools
  • Persistent cough
  • Persistent nausea
  • Psoriasis
  • Recurrent vaginal/yeast infections
  • Recurrent urinary tract infections
  • Recurrent oral thrush/bad breath
  • Sinusitis
  • Weight loss/inability to lose weight


The following tips can help you build and maintain a healthy microbiome:

  • Eat a balanced diet with plenty of green vegetables. Microbes that feed on sugars and starches are different than those that digest cellulose (found in plant cell walls). Eating a balanced diet can help to ensure that your entire microbiome is fed and that no one microorganism population overgrows another.
  • Eat probiotic foods, such as yogurt with live active cultures. These will help to introduce your microbiome to more healthy bacterial populations. Other probiotic foods to try include fermented products such as pickled vegetables, sauerkraut, and kombucha. However, fermented foods can be detrimental to those suffering from an overgrowth of yeast (including those prone to yeast infections/skin rashes/oral thrush).
  • Limit antibiotic use when possible without compromising your safety. Antibiotics are very often necessary to overcome serious infection. However, each round of antibiotics that you take sets back the health and diversity of your microbiome. If you are prescribed antibiotics, ask your doctor if they are completely necessary. He or she may say no, in which case you don’t have to take them .
  • Take a probiotic. Probiotics contain millions or billions of beneficial bacteria. Taking a probiotic once or twice a day can help to promote a diverse and flourishing microbiome. If taking a probiotic in conjunction with an antibiotic, be sure to leave at least two hours in between taking the probiotic and antibiotic, as taking them at the same time can null the effect of the probiotic.
  • Don’t shy away from dirt. Being outdoors is a great way to get fresh air and introduce your body to trillions of microorganisms. Sterile indoor environments and the frequent use of sanitizing products such as bleach and hand sanitizer can diminish the strength and diversity of the microbiome.

Choosing the Right Probiotic

There is a huge variety of probiotic supplements available, each claiming to do something different than the next. This can make selecting the right probiotic for you a difficult task. The following tips can help you best choose the most effective probiotic:

  • Be sure that the product has delayed release so that the bacteria are released in the intestine and not the stomach. Bacteria that are released in the stomach will be killed by stomach acid before ever being incorporated into the microbiome
  • Aim for a product that has multiple strains of bacteria, not just a single one. This increases the likelihood of your body incorporating one or more of the strains into your microbiome. The probiotic strains commonly perceived to be the most beneficial are L. acidophilus and B. bifidum.
  • Check the expiration date. Some health stores may stock products past their manufacture expiration date.
  • Buy a product with live cultures in it. Bacteria that have been killed by heat or sterilization processes will not do the microbiome any good.

Questions For A Doctor

You may want to ask your doctor the following questions:

  • Do you think that my microbiome could be unbalanced?
  • Do you think that the symptoms I am experiencing are the result of an unbalanced microbiome?
  • What can I do to replenish my microbiome?
  • What is the cause of my microbiome imbalance?
  • How long will it take to rebuild my microbiome?
  • Should I make any lifestyle changes to help facilitate the regrowth of my microbiome?

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