Hello. I'm Dionne.

I love food! I love using food as medicine! Most of all, I love showing others how they can use real food to regain their health. I hope you enjoy my website.

The Mysterious Microbiome

The Mysterious Microbiome

I’ve talked a lot about the importance of a healthy gut and optimal digestive system on previous blog posts.  It’s so important to the work that I do that I never complete a Nutrition Assessment without also evaluating the health of my client’s digestion.  Even if that’s not the primary reason they’ve come to me.  It’s fundamental to overall health and this is why it’s an essential component of the Rustic Diet.  One of the reasons it is so important is because the gut houses our microbiome.

What is the Microbiome

Warning: this might freak you out a little.  Particularly if you're a germaphobe.  But here's the truth you may not want to know.  90% of our cells are not our own!  That's right.  90% of our cells and 99% of our genetic material is microbial!!  This is wild, I know.  Our bodies house trillions of microbes.  Over 1000 different species.  And they're essential!  We could not be healthy, vibrant, thriving humans without this symbiotic relationship.  Actually, as you'll see below the state of our health is directly connected to the diversity of microbes we house; the more, the better.  They work industriously to affect our digestion, metabolism, vitamin synthesis, cell development, immune function, intestinal barrier function, and pathogen defenses.  This dynamic ecosystem strives towards balance every day.  Unfortunately though it is easily imbalanced by many factors; diet, medication, environment, stress.

Research from the Human Microbiome Project shows that even among healthy individuals, each person owns remarkably different types of microbes in the gut, skin, and mucosal tissue.  Each person develops a unique microbiome from birth throughout life.  We are first exposed to microbes as we travel through the birth canal, which is then hopefully followed by our second exposure in the breast milk.  By two years of age our microbiome has developed to full capacity thanks to family, food, and environment. These first exposures are critical in developing the foundation of our microbiome, which we are only now learning will influence our health throughout our life.  Interestingly, women who undergo elective cesarean have distinctly lower microbial breast milk composition as compared to women who gave birth vaginally or undergo non-elective cesarean.  Apparently, the milk bacteria and hormonal signaling during labor influence the microbial transmission into the breast milk.  That is totally amazing to me!

The Microbiome and Your Health

There is a lot of research out there on this topic.  It's definitely the sweet-heart of the research world right now.  Thanks in large part to the work of the Human Microbiome Project.  I'll try to summarize some of the more interesting findings here.  Aside from digestive influences, much of the research is looking at how the microbiome influences our immune system, brain, and metabolism.

Immune - In June of this year, The New York Times, published an op-ed piece on what we know so far regarding the microbiome and our immune system.  Simply put, the microbiome is thought to calibrate our immune system.  This in turn leads to the hypothesis that our modern-day obsession with hygiene may actually be working against us.  Delaying exposure to once common infections and improvement in societal hygiene in general may be increasing the prevalence of autoimmune diseases in our culture.  Type 1 Diabetes is an autoimmune condition of the pancreas.  There have been some studies suggesting that a lack of microbial diversity may be a risk factor for this disease.  Certain microbes give off toxins that actually stimulate our immune system better and protect against diseases like Type 1 Diabetes.  Analysis of the American Gut Project showed some correlation between gut microbiota and propensity for common allergens, both food and environmental (peanuts, shellfish, bee stings, animal dander, pollen), and even asthma.  Researchers found that participants in the American Gut Project who had allergies also had marked decreases in microbial diversity as well as greater microbial dysbiosis (imbalance).

Brain -- Another exciting area of research is around how the gut microbiome actually communicates with our brain!  Again, lack of microbial diversity seems to be correlated with increased risk for Alzheimer's, ADHD, Autism, Anxiety, Depression, even Schizophrenia.  In one interesting study looking at Hygiene and Alzheimer's Disease they actually found statistically significant relationships between Alzheimer's and areas of the world with lower levels of pathogen exposure.  Another promising study gave Lactobacillus rhamnosus GG or placebo to 75 infants for their first 6 months of life and then followed them for 13 years!  At the age of 13, ADHD or Autism was diagnosed in 6 of the 35 children in the placebo group (17.1%) and none in the probiotic group.  To continue the theme of the importance of early childhood colonization, statistically we know that children born by cesarean section and therefore missing their initial inoculation of microbes have increased risk for all the following: ADHD (300%), Autism (200%), Celiac (80%), Type 1 Diabetes (70%), Obesity (50%).

Metabolism -- This then leads us to what we know about how the microbiome affects our risk for obesity.  The research here is super interesting!  Again the benefit of diversity seems to influence metabolic regulation as well.  The types of microbes in your gut can influence energy uptake and fat storage as indicated in this study.  Another study looking at the fecal microbiota of obese versus lean twins also showed a lack of microbial diversity in obese individuals.  This was taken to the next level in this study where they transplanted the fecal microbiota from obese and lean twins into germ-free mice.  They found that despite eating the same diet the mice transplanted with the obese fecal microbiota became obese while the mice with the lean fecal microbiota did not.  For me, this is actually a really important discovery.  Working with obese clients over the years and not always having success with diet and exercise alone, gives us a third equally important avenue to explore.  By restoring microbial diversity you can actually help change your metabolism. Within the world of integrative and functional medicine, there's many case studies that show when a healthy microbiome is restored cravings and appetite are better regulated and the occasional treat isn't a total set-back. 

Along these lines there is also evidence suggesting that when the microbial diversity is disturbed by the use of antibiotics, or other medications, that this too will increase risk for obesity, especially with antibiotic use in early-childhood.  This should give us pause when we think about how western medicine approaches childhood health.  Antibiotics are often first-line defense for many common childhood ailments like ear infections, respiratory illnesses, acne, etc.

Optimizing Your Microbiome

So what do we do with this information.  How do we improve our microbiomes?  There's basically 3 stages to optimizing the health of your microbiome:  

Step 1: Avoid things that disrupt diversity.

  • Artificial sweeteners

  • Highly processed foods

  • Refined sugars

  • Inflammatory fats -- fried oils, hydrogenated fats

  • Pesticides and Genetically Modified Organisms (GMOs)

  • Antibacterial products -- soaps, sprays, etc

  • Only use antibiotics when absolutely necessary -- try natural remedies when possible

Step 2: Add factors that will increase diversity and keep the microbiome thriving.

  • Fiber -- a diet high in plant fiber naturally feeds and supports healthy microbes

  • Prebiotics -- these are foods that specifically fuel good bacteria

    • Jerusalem Artichoke, Dandelion Greens, Garlic, Leeks, Onions, Asparagus, Jicama, Banana, Chicory Root

  • Probiotics -- foods with active and live cultures will help add good bacteria

    • Sauerkraut, Pickled Veggies and Fruits, Kimchi, Miso, Tempeh, Kefir, Kombucha

  • Get your hands dirty -- gardening, let your kids play in the dirt, exposure to pets, etc.

  • Good stress management -- stress can also disrupt diversity so do what you can to keep your mental health in balance too

Step 3: For some of you, targeted support will be necessary to repair the gut or remove any lingering GI infections.  If steps 1 and 2 are not enough to get you feeling better then working with an Integrative Dietitian Nutritionist will be helpful in assessing what other factors need to be addressed.  Contact The Rustic Dietitian for a free 15-minute consultation.

Additional Resources


Human Microbiome Project

American Gut Project -- if you want to learn more about the diversity of your gut you can have your own stool analyzed


The Microbiome Diet

Eat Dirt

An Epidemic of Absence 

Brain Maker

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