Microbiome - the Good, the Bad, and the Healthy - Tiffany Weir, PhD Presentation

15 Sep 2017 1:43 PM | Anonymous

I'd first like to thank Tiffany Weir, PhD, professor at Colorado State University for presenting on this topic at the Denver Dietetic Association's September meeting. The microbiome has fascinated me on so many levels, so listening to an expert who specifically studies the microbiome was amazing. And, I'm pretty sure most people felt this way as we had record-breaking attendance compared to all of our past meetings.  

Just think, no matter what type of nutritional field you're in, the microbiome is sure to play a role in your patients' heath in one way or another. In case you missed this awesome presentation, here is a recap along with a copy of her presentation.    

 A little background on the human microbiome: 

The microbiome has been a hot topic in the biological and nutritional world over the past decade, and the information that has been uncovered through the numerous studies and mounds of research has been eye opening to say the least. 

We know that a healthy (balanced) microbiome is essential for maintaining good health in general, free of disease and negative health conditions, but what exactly is the microbiome and what does it affect? 

The microbiome is a community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment and especially the collection of microorganisms living in or on the human body. Your body is home to about 100 trillion organisms. (1)  Estimates of the number of bacterial species present in the human gut alone vary widely among studies, but it is generally accepted that individuals harbor more than 1000 microbial, species in the gut alone. (2) 

Most people have heard that the microbiome plays an important role in Inflammatory Bowel Disease and overall health of our GI tract, but some don't realize that it also plays a role in just about all parts of our health from immune function, respiratory function, asthma and allergies, metabolic conditions, and brain health to dental health, cancers and anxiety and depression.  

More fascinating, the microbiome plays such a central role in immune system development and homeostasis mainly due to the large number of immune cells that reside within the gastrointestinal tract that almost 70% of the entire immune system is in the gut (2), so you can see how maintaining a healthy microbiome is essential to keeping certain disease and conditions at bay.  

What Dr. Tiffany Weir, PhD had to say: 

The microbiome functions to keep us healthy and disruption to any of these functions may result in a variety of mild to severe health issues. What we eat can alter our gut microbiome by altering our gut bacteria, host metabolism, immune system production of pro- and anti- inflammatory metabolites, and lead to cancers and metabolic conditions.  

It's no secret that the Western diet isn't the healthiest no matter how you look at it, and when it comes to the microbiome, studies show that a Western diet (that is low in fiber, fruits, vegetables, and whole grains and unsaturated fats) will lower the good bacteria (Bifidobacterium, Lactobacilli, Eubacteria – to name a few) essential for a healthy (balanced) microbiome and actually increase the less-favorable bacteria. A gluten-free diet has also been shown to do the same. On the other hand, the Mediterranean diet has been shown to increase the good bacteria supporting a well-balanced microbiome. Here's how specific macronutrients affect and interact with the microbiome. 


The gut microbes primary source of energy is carbohydrates. And, through the microbiota metabolism, undigested carbohydrates are converted to fiber which is then fermented and short chain fatty acids (SCFA) are produced. SCFA show to stimulate proliferation of normal crypt cells, and inhibit growth of colon cancer cells, as well as, reduce the risk of developing inflammatory bowel diseases such as Crohn's and Ulcerative Colitis. Therefore, carbohydrates including fiber are an important part of maintaining colon health. 


Animal protein which contains significant amounts of Choline and Carnitine have been shown to have a negative effect on our health and the microbiome. Trimethylamine N-oxide (TMAO) is a small colorless amine oxide generated from choline, betaine, and carnitine by gut microbial metabolism, which raises the risk of cardiovascular disease (CVD). Animal protein has also been shown to reduce the good bacteria in our gut and SCFA. 

Plant protein on the other hand, has been shown to increase good bacteria, increase gut barriers (preventing leaky gut), reduce bad bacteria and reduce inflammation, reducing the risk of CVD and IBD.  


Studies suggest that they type of fat consumed has a significant impact on the microbiome.  Diets high in unsaturated fats have been linked to an increase in good bacteria, while diets high in saturated fat have been linked to a decrease in good bacteria. 

When concluding the diet portion of her presentation, Dr. Weir mentioned how fermented foods are high in good bacteria, but finding those foods are hard to come by. Canned and jarred foods like sauerkraut, and pickles have been pasteurized, so they lack the live cultures that benefit the microbiome. Kimchi, kefir, yogurt (that says live cultures) and kombucha on the other hand are great for boosting your microbiome. 

She also mentioned that taking a quality pre/probiotic can be beneficial, but the market is saturated with less-than quality products making it hard to find one that will work. She suggested taking medical food vs a dietary supplement, but the downfall to this is that medical food is hard to come by. It is usually prescribed by a doctor.   

Eating a well-balanced diet full of fruits and vegetables and whole grains, healthy fats and fiber still appears to have the best health benefits of all. 

 Additional Observations in Regard to the Microbiome: 

Dr. Weir also touched on the difference in microbiomes between breast-fed and formula-fed babies, stating breast-fed babies have more good bacteria and better immune system support due to higher levels of oligosaccharides in breast milk. 

Current and Future Trends for Creating a Healthier Microbiome 

There are a lot of new trends and practices coming to light that aim to support a healthier microbiome and prevent/cure diseases and conditions, and one that I've personally read a little about is showing a lot of promise.  

It is the swabbing of babies born via C-section called vaginal microbial transfer. Studies show that babies born vaginally have a healthier microbiome will be at lower risk than C-section babies for developing allergies, asthma, type-1 diabetes and obesity later in life. Samples of microbes from the mother's vagina are collected before delivery and swabbed (or rubbed) all over the infant within minutes after delivery exposing the baby to many essential and beneficial microbes.  

Another rising procedure is Fecal Transplant. Just as it sounds. This procedure takes fecal matter from a healthy donor and is placed in a person with a disorder or condition. Usually, this treatment is used on patients with C. Diff., or a type of IBD. 

There are also tons of other paths being followed to obtain a healthier microbiome. Functional medicine, diagnostic platforms, genetically engineered probiotics, supplementation with butyrate, custom therapeutic solutions, gene sequencing. 

I've attached a copy of Dr. Weir's presentation here. 



1. https://www.genome.gov/27549400/the-human-microbiome-project-extending-the-definition-of-what-constitutes-a-human/

2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4566439/ 

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