The Microscopic Organ That Secretly Controls Your Child’s World

By Madiha Saeed, MD

While your child may pretend he’s a superhero, did you know that he is actually a super-organism? That’s right—human beings are super-organisms, made up of a complex blend Superhero kidof genetic traits from human and microbial cells that control and influence our world. Our 10 trillion human cells are outnumbered by 100 trillion microbes—that’s about 3.5 to 4.5 pounds of microbes in our digestive system alone! Can you imagine? Could these tiny stowaways be controlling our genes? Influencing our moods? Determining whether we are sick or healthy?[1]

A child’s DNA isn’t her destiny. Instead, her environment, especially the microbiome (all the microbes in and around her body), influences her gene expression. Genes may load the gun, but our environment and lifestyle choices pull the trigger. Encoding about 3.3 million non-redundant genes (out of more than 10 million identified), the microbiome can be viewed as a “new organ” playing a vital role in our health. It is unimaginable, but true, that something so microscopic can influence so much! Mind blowing!

What determines our microbiome? We are one with our environment.

When a child is born into this wonderful world, he begins to acquire information from new stimulus in the environment. One of the most important forms of new stimulus is the microbes that first interface with the body. A newborn baby dbacteria-2oes not yet have established colonies of bacteria or other microbes on the skin, lungs, or intestines. When he passes through the mother’s birth canal, he begins to acquire bacteria and other microbes from his mother and the outside world, and his gut begins a harmonious and beneficial relationship with more than a thousand strains of symbiotic bacteria. The modern Western lifestyle (what we eat, how we live, the choices we make) is one of the most important factors influencing our microbiome and may be responsible for inflammation leading to chronic diseases. Here are some of the primary ways that we acquire our microbiome:

Our mamas: delivery and beyond. Initial inoculums of microbiota from the mother occur during birth and our bodies begin a harmonious and beneficial relationship with more than a thousand strains of good bacteria. In a vaginal delivery, the microbiome develops species similar to the mother’s vagina and gut. In a cesarean section, the microbiome develops predominant species similar to skin flora of the hospital attendants and the mother and have an increase in the chance of childhood chronic disease like asthma, allergies and autoimmune diseases.

Breastfeeding contributes to a microbiome that looks different from the microbiome of formula-fed infants. These microbial differences can ultimately influence gene expression and physiological changes that impact everything from metabolism to immune function.[2] The microbes we acquire at birth affect our health throughout our lives. Who knew that early exposure to microbes can influence so much?

We are what we eat. Yes, that burger or veggie that you eat can affect the composition and metabolism of our microbiome, which is directly related to our health as we could be feeding the good or the bad bugs.[3] A high fiber, nutrient-rich diet can increase beneficial bacterial colonies, enriching the microbiome, while eating the wrong foods can create an inflammatory effect leading to chronic disease (so put down that soda). When we eat, remember that we are eating for 100 trillion, not just one.

Chronic stress (emotional or social), that includes work and our inlaws, can raise stress hormones (CRF) that negatively impact the microbiome, which in turn, alter gut permeability, lead to inflammation, and ultimately influence our epigenetics[4]. This connection also works vice versa, as the wrong microbes can talk back to the brain and create more stress and inflammation. Something to keep in mind next time you host a family reunion (kidding).

Environmental contaminants. (Xenobiotics/pesticides, antibacterial products and other chemicals) There tens of thousands of synthetic chemicals that are anti-microbial or that can harm our internal microbes. Think about this every time you use a disinfectant product.

Use of medications. Common pills we pop, including NSAIDS (like ibuprofen), birth control pills, steroids (like asthma medications), antibiotics, chemotherapy drugs and radiation therapy, antidepressants, antipsychotics, drugs used for sleep, acid-blocking drugs, opiates and other pills can all impact our microbiome negatively. So always think twice before you take a pill. Weigh the risks versus the benefits of the particular medication and keep an eye towards replenishing or restoring the microbiome if you must take one.

How the bugs affect us.

Our microbiomes have innumerable functions, playing an important role in digestion, metabolism, immune and defense functions among others. For a healthy immune system, the body is dependent on a good relationship with the beneficial bacteria that live in the digestive tract, and are also involved in:

  • Gene expression. Immediately after birth, there is a profound and dynamic interaction between the host and microbiome that affects genetic expression. The absence of healthy gut bacteria alters genes and signaling pathways involved in learning, motor control and memory, changing host cellular functions. Sequencing the genomes of our own microbes (our second genome) is essential for understanding the human condition.[5] Isn’t that fascinating!?
  • Disease. Negatively affecting the healthy microorganisms residing in our gut may deregulate genes mediating energy-metabolism-producing toxins that mutate DNA, allowing pathogenic organisms to thrive, leading to intestinal inflammation and bacterial dysbiosis. Dysbiosis (gut microbial imbalance) affects human epigenetics and has been linked with important human diseases, including autoimmune disorders and metabolic disorders, such as obesity, type 2 diabetes, allergies, cancer and neurological disorders.
  • Mood and behavior. The microbial composition influences behavior by inducing changes in the expression of certain genes, activating enzymes and altering the neural signals in the enteric nervous system. The microbial composition can stimulate the vagus nerve which can either cause stress or a calming response. Negatively altering the microbiome can also lead to cytokine release, increasing stress and inflammation leading to mood disturbances, stress, anxiety and sleep issues. So now when your child is in a bad mood, we can (partly) blame it on the trillions of bacteria that live in their world?
  • A healthy microbiome is gastro-protective and will prevent inflammatory bowel conditions but is also involved in regulating peristalsis, reducing intestinal inflammation and protecting gums and teeth.
  • Nutrition. The microbiome manufactures vitamins B1, B2, B3, B5, B6, B12 and K, increases absorption of minerals, minimizes or eliminates lactose intolerance, aids in protein digestion and manufactures essential fatty acids and short chain fatty acids.
  • Immune regulation. A healthy microbiome helps to break down bacterial toxins, protects against toxic substances, has antifungal, antiallergenic, anti-infective, antiviral, anti-proliferative, immunomodulatory effects.
  • Weight control. When your gut microbiome is balanced it decreases inflammation, tells genes to burn fat rather than store fat, regulates the harvest of calories from energy extraction from food and produce short chain fatty acids which have incredible weight-loss properties. An imbalanced microbiome can cause weight gain and obesity, provoke inflammation, create insulin resistance, worsen food sensitivities and leaky gut, create hunger and cue your genes to hold onto fat.
  • Other body effects. A healthy microbiome is cardio-protective, supports healthy blood pressure and normalizes serum cholesterol and triglyceride levels. It also acts as an antioxidant, antidepressant and breaks down and rebuilds hormones.


With trillions of tiny organisms invading our children’s bodies and influencing everything down to their genetic code, it is empowering to think that every bite we feed our children can have a profound impact on their health! So the next time your child puts on a cape, remember the secret microscopic organ that controls your child’s world. As your little superhero is actually a superorganism! So fascinating!!

What daily methods do you implement to ensure a healthy internal and external world for your child and their trillions of friends?


[1] Martin J Blaser, MD J Clin Invest. 2014; 124(10): 4162-4165.

[2] Mona Mischke, Torsten Plösch American Journal of Physiology – Regulatory, Integrative and Comparative Physiology, Published 15 June 2013, Vol 304 no. 12, R1065-R1069 DOI: 10.1152/ajpregu.00551.2012

[3] David Turnbaugh, et al (Harvard Medical School), Nature 2014 Vol 505: 559-563

[4] Expert Rev Gastroenterol Hepatol. 2014 Aug; 8(6): 583–585

[5] Front Microbiol. 2011 Vol 2(166): 1-14)


  1. Susan Levin

    This is so terribly important. My children both have ADHD so gut health is of paramount importance around here! Our main interventions are the Body Ecology Diet and regular exercise. We also do regular parasite cleanses, as well as probiotics (mainly through fermented foods but also supplements). It never ends. I’m so grateful I know about gut health and can give my kids a solid foundation for a healthy life!

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