Gut Microbiome 101

Gut Microbiome 101

Our bodies are complicated, fascinating machines composed of human and non-human parts that come together to make us these super-organisms. Your body performs a bazillion (ish) functions every minute! I’ve always thought it is a wonder more things do not go wrong…

“Wait, back up T – did you say my body has NON-human parts?”

Right, let me explain. We are not just human cells. In fact, we are MOSTLY bacteria, which are totally separate organisms with their own, non-human DNA. Loads of bacteria live inside and outside of our bodies. Your skin, your mouth, your eyes, and your digestive tract are covered in bacteria, and they play a VITAL role in your health. This is why it is so important to understand how your lifestyle and genetics affect the health of these bacteria, in particular, the ones located in your gut.

Read on, and you’ll learn:

  1. The effects your gut microbiome has on your health and wellbeing, and
  2. The dietary and lifestyle actions you can take to heal and restore it!

What is the gut microbiome?

If you take a little journey down your esophagus into your digestive tract Magic School Bus-style, you’ll find a TON of bacteria that set up camp in your intestinal tract. These bacteria comprise the “gut microbiome.” The majority if these bacteria reside in your large intestine (i.e. your colon). Say hello to the 1000 bacterial species inside of you that encode about 5 million genes (1) and perform an INCREDIBLE amount of functions in your body (e.g. immune system, brain health, making vitamins and other compounds, response to vaccination, hormone regulation, digestion, nutrient absorption, etc.).

However, when the gut microbiome isn’t healthy, its ability to perform those functions is compromised, which can lead to these conditions:

  • Inflammation
  • Obesity
  • Allergies, asthmas
  • Skin conditions
  • Brain fog
  • Fatigue
  • Depression
  • Bone health
  • Thyroid conditions
  • Autoimmune disease
  • Digestive disorders

So, how does this work?

The microbes (bacteria) in our colon have access to items that we eat that are poorly digested by our own digestive enzymes or poorly absorbed in the small intestine. These foods are primarily fiber from plants, other polyphenols (plant nutrients) and complex carbohydrates (2). They fuel the metabolism of the microbiota. When the microbiota aren’t fed well and in balance, we start seeing some problems manifest.

For example, a diet high in refined sugars and carbohydrates will feed SOME bacteria, but essentially starve the others. The bacteria that really like those sugars will actually send signals to your brain to consume MORE of those foods, too. You literally are not controlling your own cravings! Proper hunger signaling cues get disrupted and as the other bacteria continue to get starved, they become less efficient and able to perform functions appropriately, creating problems like inflammation and indigestion.

If this inflammation continues chronically, people start developing problems in different ways. Some people may have acne or eczema, others may have brain fog, fatigue, and/or low energy, and others may develop more significant issues such as irritable bowel syndrome, autoimmune conditions, or even Type II diabetes.

Just to be clear, having a compromised gut is not necessarily the ONLY culprit in driving these problems, but it often contributes.

You’ve heard of fecal transplants too, right? It’s a process where a healthy donor gives fecal matter (go ahead and google “fecal” if you need to) from their colon, with all their bacteria, to a sick recipient. This treatment has shown HUGE improvements in metabolic markers for the recipient due to the donor’s healthy bacterial influence.

We need a certain amount of particular types of bacteria in our gut to facilitate good health.

The Western world has lost a lot of species and diversity that was once much more prevalent, largely due to these common trends:

  • Poor diet-high in refined carbohydrates, sugars, industrial seed oils, and low in fiber
  • Not sleeping enough/poor sleep
  • Overuse of antibiotics
  • Overly sanitary environment
  • Lack of exercise

The Importance of early bacterial exposure

We are born basically sterile, and so the development of the microbiota begins immediately at birth. There has been a lot of research around how the type of birth and feeding practice an infant goes through affects this development. There tends to be a more beneficial microbial colonization that happens with a vaginal birth and breast-fed infants (2). Connections have been made with infants that went through a C-section and formula-fed that have less than ideal gut health. Ramifications of this could include compromised immune systems, allergies, skin conditions, ADD/ADHD, food sensitivities, or other problems related to an unhealthy microbiome (2,3).

I want to note that a person that goes through either of these as an infant is not necessarily going to have a terribly compromised gut, nor is a person that had a vaginal birth and breast-fed going to have a pristine gut. Nor do I think we should judge mothers who have taken these routes.  However, they CAN make a huge difference in the development of your microbiome, and the more everyone knows about the costs and benefits of these choices, the more empowered our decisions will be

You can imagine that if we go through childhood into adulthood with continued poor care of our gut, more problems will occur and manifest in a variety of ways.

So how can we help heal our guts?

Elimination diets, such as the Whole30, lay the groundwork for “resetting” our gut. In my opinion, these dietary interventions may be necessary for much more than 30 days depending on your condition.

Eliminating potentially problematic, irritating foods – such as wheat, dairy, soy, alcohol, and industrial seed oils — can help restore the bacteria in our gut.. This isn’t to say the treatment is forever, but many of us need to repair and restore our gut, and this really can’t be done entirely without taking away these irritants long enough for the body to recalibrate its optimal balance of gut bacteria.

If that seems a bit too drastic for you and you aren’t symptomatic, perhaps try incorporating more fiber into your diet through higher intake of colorful fruits and vegetables, and possibly a probiotic (more on this later, though. Not all are created equal!). Fermented foods can be great too. I will post another blog detailing more about prebiotics as well, but for now, you can try out some fermented foods like kimchi, kombucha, or sauerkraut.

Additional damaging agents to avoid include antibiotics, too much sanitation (think more dirt exposure, not more public bathroom exposure…) and environmental toxins like heavy metals, pollutants, and chemicals in cleaning supplies. It is hard to remain completely abstinent from all exposure, but having an awareness and understanding how to mitigate exposure will help.

Did you know it can actually be very beneficial for your child’s microbiome development if they grow up around animals and play in the dirt? Think about joining them next time if you can. “Live dirty, eat clean” was one of my favorite quotes in this awesome talk about the microbiome.

It is amazing what can happen when a person works to restore the health of their gut and how many of these problems seem to vanish or decrease significantly! I have seen it first hand with many of my clients, myself included.

This is just the tip of the iceberg in terms of all the incredible research around the gut microbiome and effects on your health, but I hope it served as a good introduction for you all. Let me know if there are questions and again, PLEASE feel free to recommend any other topics you want covered!  You can email me by clicking the “Contact” link at the top of the page.


Therese Martinez, MS, RD, CPT



  1. D’Argenio, Valeria & Salvatore, Francesco. The role of the gut microbiome in the healthy adult status. Clinica Chimica Acta. (2015) Clinica Chimica Acta 451 (2015) 97–102
  2. Kresser, Chris. RHR: Is a Disrupted Gut Microbiome at the Root of Modern Disease?-with Dr. Justin Sonnenburg. May 12, 2016.
  3. Weiler, Nicholas. UCSF: Newborn Gut Microbiome Predicts Later Allergy and Asthma, Study Finds; Microbial byproducts link particular early-life gut microbes to immune dysfunctions. September 12, 2016

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