Meet Your Newest Trillion Best Friends

Therese Martinez

Today I want to take you on a journey. A journey toward getting to know yourself quite a bit better. In fact, this journey will introduce you to the trillion bacteria living inside of you right this moment. We are going to go into your mouth, down your esophagus, through the stomach, into the intestinal tract, stop in the small intestine, and set up camp primarily in the colon. This, my friends, is your gut microbiome. 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. Some now even consider it the “forgotten organ” (2). I have been fascinated with the research around the gut microbiome for a while now, and hope to spark some interest for all of you as I dive into the effects that the condition of your gut microbiome has on your health and wellbeing. It will be important to understand what helps and what hurts our gut microbiota and what we can do about those external influences to best aid in making our body feel and look AMAZING!







Lets just look at some of the topics that have been found to correlate with the health of the microbiome and your body:


  • Immune system
  • Encode proteins/enzymes for a host of responsibilities in the body
  • Brain health (affected by chemical signals from microbes
  • How we respond to vaccination
  • Inflammation
  • Obesity
  • Allergies, asthmas
  • Skin conditions
  • Brain fog
  • Fatigue
  • Depression
  • Bone health
  • Hormone regulation
  • Thyroid conditions


The human body is an ecosystem composed of microbial and human parts that come together to make us this super-organism. Microbes mostly live in the colon, the end of our digestive tract, so they only 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 and complex carbohydrates (2). They fuel the metabolism of the microbiota. It is important for our gut to maintain a balanced, well-fed microbiome so that it can properly perform all of its functions. There is actually quite a bit of evidence associating people that have a lower diversity of microbiota with worse metabolic health and higher markers of inflammation. When these same people get put on dietary interventions that increase the diversity, those health markers improve (2). You’ve heard of fecal transplants too, right? The process where a donor gives fecal matter (you know, from their colon with all that bacteria) to a sick recipient? This treatment has shown HUGE improvements in metabolic markers for the recipient due to the donor’s healthy bacteria influence. 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


Other potential influences include:

  • Travel
  • Illness
  • Hormonal cycles

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. However, they CAN make a huge difference in the development of your microbiome.

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. Relating back to my first list, this could include:

  • Skin conditions: eczema, rashes, acne
  • Fatigue, brain fog (how much caffeine do you really need a day?)
  • Digestive issues- IBS, bloating, cramping, diarrhea, constipation
  • Worsening pain/symptoms with autoimmune conditions- increased flare-ups/pain with Rheumatoid Arthritis, osteoarthritis, multiple sclerosis, etc.
  • Heart disease
  • Depression
  • Autoimmune conditions (new research is even out on the relationship of Type I Diabetes and the gut!)


At the root of many of these manifestations and diseases is chronic inflammation. When our gut microbiome has been damaged chronically through poor diet, antibiotics, high stress, travel, sanitation, etc., the bacteria diversity and flora are imbalanced and functioning less than ideal. For example, if the gut microbiota is fed dietary fiber (which lacks in a Western diet), it ferments that fiber and creates short-chain fatty acids that are absorbed and actually have an anti-inflammatory effect in the body (2). When we lose this process, we gain inflammation, and many of the aforementioned conditions are driven by inflammation. This is just ONE example, remember. There are many other issues that occur that drive inflammation when our microbiome is compromised.

I want you to think about the medications you are on or have taken in the past. What were they treating? Have you tried other types of interventions (dietary or supplements) to treat the conditions instead? I’m definitely not anti-pharmaceuticals. I am a type I diabetic, after all. But, I do believe in your body’s ability to heal itself when given the nutrients it needs.


So how can we help heal our guts?

Well, some of you may have heard of the Whole30. This dietary intervention lays a lot of groundwork for “resetting” our gut. Elimination diets such as this one are more than just diets, and in my opinion, may be necessary for much more than 30 days depending on your condition. Eliminating potentially problematic, irritating foods can help restore the bacteria in our gut. Foods like wheat, dairy, soy, alcohol, and industrial seed oils. 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 for a time being. If that seems a bit too drastic for you and you aren’t symptomatic, perhaps try incorporating more fiber into your diet, and possibly a probiotic. Fermented foods can be great too. I will post another blog detailing more about prebiotics and probiotics, but for now, try out some fermented foods like kimchi, kombucha, or sauerkraut (all fresh of course!). Feel free to ask me for recommendations on any of that.

images-8Additional damaging agents to avoid include antibiotics, too much sanitation (think more dirt exposure, not more public bathroom exposure…) and environmental toxins. 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.

This was 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 posed a good introduction for you all. Let me know if there are questions and again, PLEASE feel free to recommend any othr topics you want covered!


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
Therese Martinez, MS, RD, CPT

1 Comment

  • Therese Martinez
    Lionel Liberty
    February 23, 2017 7:59 pm

    Embracing my gut health has changed the way I live day to day. I have more energy, can accomplish more in a day, sleep better, and overall my relationships and morale are ay an all time high in terms of positivity.

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