Microbiome Alterations

Humans are interesting creatures with an interesting makeup. Each of us is comprised of 10% human cells and 90% microbial cells. Your microbiome is incredibly complex and vital to your health. It consists of approximately 100 trillion bacteria, viruses and fungi, mostly residing in your gut (for context that is over 12,000 times the number of people on earth).

Your microbiome regulates most of your body’s physiological events. It plays a critical role in many processes including;

• immunity development
• ongoing protection from harmful microorganisms
• production of short-chain fatty acids, which are a source of energy
• vitamin synthesis (particularly B vitamins & vitamin K)
• amino acid (and protein) synthesis
• fat metabolism
• mood and behaviour regulation
• nervous system regulation

Your gut microbiome also plays critical roles in how medications are metabolized by your body. It can affect your response to medications. Your microbiome can alter a drug’s activity in your body, toxicity, or bioavailability, which is the extent and rate at which the drug enters your bloodstream. This can have profound implications on drug activity, effectiveness, side effects and safety.

We have known for centuries that what we eat and what medications we take impact our health. For decades scientist believed that what you eat and the drugs you take could have a profound impact on your microbiome and intern your health.
Thanks to two new studies we now know that your microbiome is deeply affected and potentially permanently altered by the foods you eat and the drugs you take.

Food Additives

The first study (published WHERE? In July 2020) looked at how artificial food additives affected the microbiome. Food additives are ubiquitous in our society. They are the ingredients added to foods to improve color, taste, smell, nutritional value, and shelf-life. Approved additives used in North America and Europe have undergone animal safety studies and are assumed as safe, however new techniques indicate some of them have health concerns.

They found that the artificial ingredients did alter the microbiome in many cases with negative health outcomes. They found emulsifiers were linked to obesity-related intestinal inflammation and liver dysfunction. Use of artificial colour led to changes in bacterial population and DNA damage. Flavour enhancers enhanced fat accumulation and fat deposition in muscles. Artificial sweeteners were found to destroy glucose tolerance and support weight gaining by negatively affecting the microbiome.

The research outcomes were not entirely negative. The same research found that naturally occurring thickeners had positive impacts on the microbiome. Thickeners were able to reduce intestinal inflammation and improve intestinal barrier function while increasing free fatty acid production.

Medications

The second study (published WHERE? in September 2021) looked at how medications interacted and affected the microbiome. Researchers looked at some of the most widely used classes of drugs – those for depression, diabetes, and asthma – to see the effects.
This is a relatively new field of study. It is widely known that microbiome bacteria have the ability to control the availability and effectiveness of medications. Researchers theorized the main underlying mechanism as the chemical transformation of drugs by microorganisms (the process called biotransformation). What they discovered was substantially different. They found a significant number of the drug-bacteria interactions were due to bioaccumulation; “that is, bacteria storing the drug intracellularly without chemically modifying it, and in most cases without the growth of the bacteria being affected.” They provided one example where one drug (duloxetine) binds to several metabolic enzymes and changes the metabolite secretion of the bacteria itself.

The researchers concluded that medications can often accumulate inside microbiome bacteria, altering bacterial function. One outcome resulting from this is potentially altering drug availability and bacterial metabolism. This intern can alter microbiome and individual bacterial composition, pharmacokinetics, side effects and drug responses, with the affects most likely unique to each individual.

The last comment ‘most likely unique to each individual” is of grave concern. By being unique, there is no predictive nature to what affect a given dose of a medication will have on an individual. Will 10mg of “medication A” be enough to treat “patient 1” as it was in “patient 2” with the same diagnosis? Or will 10mg be far too high, with dangerous side effects? How will your doctor know, before they prescribe?

Your Microbiome
These are steps you can take to help nourish your healthy microbiome.
■ Eat fresh fruit and vegetables, particularly green leafy vegetables.

Whole fresh fruits and vegetables (not cooker, processed or juiced) are packed full of vitamins minerals and fibers to support your body and microbiome. Eating a wide variety daily will help reduce your risk of infection.

■ Reduce sugar and processed foods

Sugars get digested very quickly (leading to blood sugar spikes which in turn leads to blood sugar issues). So quickly are they digested that the healthy bacteria in your microbiome can’t use them as a food source. If you eat too much sugar regularly, you run the risk of literally starving your microbiome to death. If they don’t have enough food, they will resort to feeding off the lining in your intestine, which can lead to inflammation.

■ Severely reduce foods with artificial ingredients, especially artificial sweeteners and emulsifiers

Artificial sweeteners and emulsifiers may work to make food more appealing, but they wreak havoc on your microbiome, leading to blood sugar, weight, and inflammation issues.

■ Use probiotics every day

Probiotics are the live bacteria that work to keep your microbiome healthy, happy and working efficiently. Supplement each and every day to make sure you are helping your microbiome. Ideally you want to choose a probiotic that is clean and free of any unnecessary additives or chemicals. Look for one that is vegan and certified both kosher and organic. This will ensure you’re getting one that is truly clean.

■ Stock up on prebiotics every day

Prebiotics are the food for your microbiome. These specialized fibers are the food that the probiotics in your microbiome need to stay healthy and work for you. Again look for one that is vegan and certified both kosher and organic. This will ensure you’re getting one that is truly clean.

■ Enjoy fermented foods

Fermented foods are gut-friendly helpers for your microbiome. These foods naturally contain probiotics (albeit normally in small amounts). Add a variety of fermented foods to your diet to regularly add probiotics on top of your daily supplement. Try a combination of products; yogurt (unsweetened), kefir, kimchee, kombucha, pickles, and sauerkraut.

■ Avoid antibiotics

If probiotics are your microbiome’s best buddy, then antibiotics are your microbiome’s sworn enemy.
Antibiotics have one very simple job, kill bacteria. This is great when you are fighting a bacteriological infection (strep throat or urinary tract infections), but very bad all other times. Antibiotics cannot recognize the difference between good gut bacteria and bad bacteria. They just kill all the bacteria including those working for your good health in your microbiome. Try to only buy meat, poultry and fish products that were raised without antibiotics. If you do need to take an antibiotic to treat a specific condition, make sure to double (or even triple) up your daily probiotic and prebiotics for the duration of your prescription and for several weeks after to help replenish your lost gut bacteria.

■ Exercise regularly

Physically active people have more healthy and diverse microbiomes than inactive people. Every little bit helps. Even just walking for 30 minutes a day could have a profound impact on your gut health.

Gultekin F, Oner ME, Savas HB, Dogan B. Food additives and microbiota. North Clin Istanb. 2019;7(2):192-200. Published 2019 Jul 17. doi:10.14744/nci.2019.92499

Klünemann, M., Andrejev, S., Blasche, S. et al. Bioaccumulation of therapeutic drugs by human gut bacteria. Nature 597, 533–538 (2021). https://doi.org/10.1038/s41586-021-03891-8