Decoding & Understanding Your Gut Microbiome
Nuts & Bolts
First, let’s provide some definitions so were are all on the same page.
Microbiome = general term for all of the microbes (bacteria, viruses, fungi, yeast, etc.) that live inside us (gut, nasal, lungs, vagina) and on our body (skin).
We seed our microbiome at birth by passing through the vaginal canal and from breast feeding.
We see different microbiomes and higher incidents of certain diseases (e.g., autoimmune) when infants are not born vaginally or not breast fed.
Chronic or repeated use of antibiotics, especially in children/young adults, are associated with dysfunctional microbiomes.
Aging - we see a decline in microbiome diversity, which is also thought to contribute to natural decline in our immune system’s ability to fight infections as we age.
Prebiotic = plant fibers that feeds commensal bacteria/microbes in your gut. What microbes are fed significantly impacts what they produce and the quality.
Probiotic = foods that contain live microbes. Probiotic supplements have a combination of living microbes, prebiotics to feed the microbes, and post-biotics the microbes produce.
Post-biotic (aka microbial metabolites) = what the microbes produce when you feed them probiotics.
There are many beneficial metabolites such as neurotransmitters (e.g., serotonin, GABA, dopamine) and short chin fatty acids (e.g., b-hydroxybutyrate, propionate, acetate) which regulate hormones, appetite, blood pressure, mitochondrial function, and inflammation.
This is one example of the Gut-Brain axis interaction and why neuroinflammation, neurodegenerative diseases, and mental health are influenced by the gut microbiome.
Symbiotic = combination of probiotics + prebiotics.
Misconceptions, Misinformation, and Common Questions
Next, let’s address some common misconceptions, misinformation, and questions about the gut microbiome and different “-biotic” supplements.
Probiotics are not permanent and at most, only last ~24hrs.
Taking probiotics to address GI related issues is only treating the symptom and not the cause. Even more, this is really just making expensive poop!
Solution: to support a healthy gut microbiome, you need to adopt certain lifestyle factors like eating foods that feed beneficial microbes so they have a hospital environment to live in your gut.
Top 6 prebiotic foods supporting beneficial gut microbes: Jerusalem artichokes (aka sunchoke), leeks, raw chicory root, onion, garlic, and dandelion greens.
At best, any single probiotic strain works for about 3 months maximum before your body becomes resistant to that strain and it no longer has beneficial effects.
Solution: Take a break and switch up strains seasonally. This allows strains to continue to have benefit over the long run.
When might you use probiotics and who would benefit the most?
When you’re taking oral antibiotics, taking a probiotic can help reduce GI symptoms from the antibiotics (e.g., diarrhea, gas, bloating). Once you finish the course of antibiotics, stop taking probiotic to let your gut repopulate. Eat good prebiotics (e.g., fermented foods) for 1 week and then return to your “normal” diet.
Prebiotics post-surgery: because of 1) anesthesia (impact can last for 4-9months), 2) exposing anaerobic environment to air, and 3) usually get antibiotics prophylactically
Older adults (>50yr) or immune compromised individuals are at a higher risk for developing C. difficile overgrowth after a course of oral antibiotics. Taking probiotics while taking antibiotics can help lower the risk of developing C. difficile overgrowth in higher risk populations.
What probiotics are not:
Not effective at correcting underlying symptoms resulting from an unhealthy diet (e.g., Standard American Diet).
Not a solution to what is causing GI symptoms like cramps, gas, bloating, indigestion, diarrhea, or constipation.
Not a “consequence free” way to continue eating foods that give you GI issues or to which you have immune reactions.
Not a magic bullet for fat loss.
Anytime a product is marketed as a "magic” bullet and makes broad promises or claims, this should raise a red flag. Your body is amazingly complex and always changing, so having a single solution is not only short sighted but illogical.
Different strains for Different folks
We are still discovering the complexities of the gut microbiome and are learning it varies significantly between each individual. Certain strains can be used to manipulate the immune system and help restore balance but only when combined with essential healthy lifestyle factors.
There are so many factors that affect your gut microbiome (environment, genetics, lifestyle, maternal, etc.). We don’t yet know what is the best combination for each individual because each person is different and this can change as you age.
For example, Lactobacillus strains can worsen symptoms in some people and improve symptoms in others.
Some studies have shown kefir may lead to more permanent Bifidobacterium strain repopulation but dairy based kefir is not recommended those with neuroinflammation (Parkinson’s disease, TBI, Alzheimer’s, etc.).
So how do you maintain a healthy gut microbiome?
What you eat is the #1 most effective way to maintain a healthy gut microbiome. Eating 30 different plant-based whole foods a week is the target goal and effective amount to achieve the variety needed.
Smoothies are a great way to achieve this diversity.
Make it a game to eat different plants throughout the week. Strategies: eat the rainbow, eat seasonally, and try new recipes.
Exercise is essential because this is how those beneficial metabolites move from the gut into the blood where they circulate to other tissues (e.g., brain).
Breaking a sweat (e.g., Zone 2 heart rate) is the sweet spot. Doesn’t have to be high intensity but exercising the spectrum of your heart’s zones in moderation is good for the cardiovascular system. Again, variability is important to stimulate the full spectrum of cardiovascular system’s capabilities. Too much of high intensity doesn’t allow recovery and can lead to excess inflammation.
Sleep is important for your gut microbiome because cortisol
7-9 hours per night
Sleep hygiene strategies: meditation, breathing, no screens 1hr before sleep, maintain consistent sleep/wake schedule even on weekends, blue light blockers/reduction (glasses, apps, LED bulbs), vagal nerve stimulation, acupressure mat, red light therapy/dry sauna, warm bath/shower before bed to raise core temperature, and a dark, quiet, cool room for sleeping.
Stress reduction – cortisol levels regulate our immune system and are important in keeping immune system in balance. Well know that stress causes inflammation, weakens immune system, and has negative impact on gut micrbiome
Strategies: meditation, spending time in nature, breathing strategies, vagal nerve stimulation, acupressure/acupuncture, massage, etc.
Tips to be an informed consumer
Considerations for selecting healthy fermented foods
Fermented foods have living microbes, they do not contain probiotics unless those are added by the manufacturer.
It is easy and inexpensive to make your own. Store bought products are higher in sugar, which is known to cause microbiome imbalance, and not currently required to disclose what the microbes are fed. Avoid purchasing higher sugar fermented foods (e.g., yogurt, kombucha, kefir) and try to buy the ones with less sugar.
People with hypertension or cardiovascular disease should be cautious about high salt fermented foods (e.g., miso, kimchi, pickles). These individuals can either make their own fermented foods to control sodium levels, select low sodium options, or eat other fermented foods that do not have sodium.
Key Take Aways
Probiotics are helpful at reducing the risk of developing an overgrowth of harmful microbes (e.g., C. difficile) when taking antibiotics, especially for higher risk populations (elderly, immune compromised).
Probiotics are not a magic fix for an unhealthy diet or GI issues because they do not address the underlying cause(s) of these issues. Don’t treat the symptom, treat the cause.
How to maintain a healthy gut microbiome:
#1 Eat 30 different plant-based foods per week. Challenge yourself to not get stuck eating the same foods over and over. Limit/avoid sugar, alcohol, charred foods, and any foods you don’t tolerate because as these are detrimental to your gut microbiome.
30-45 minutes of daily exercise (enough to break a sweat) to circulate the beneficial post-biotics from your gut microbiome
Get 7-9hrs of sleep each night
Practice stress reduction techniques to reduce promotion of inflammatory processes
Play in the dirt (gardening, being outside)
Having a pet (self-groomers – cats, dogs)
Additional Resources
Books about the gut microbiome
Podcasts
Phoenix Helix Podcast has many episodes, here’s one example.
