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Your microbiome, the community of around 100 trillion bacteria, viruses, and fungi inhabiting your gastrointestinal (GI) tract, plays a pivotal role in health and disease.
The microbiome has been implicated in multiple chronic conditions ranging from inflammatory bowel disease, type 2 diabetes, and cardiovascular disease to colorectal cancer.
Your microbiome has a direct impact on how you think, feel, and act too.
We know that the gut microbiota undergo significant fluctuations over the course of one’s lifetime … and these modifications are frequently associated with undesirable effects on your health.
But, these fluctuations are influenced by several controllable factors, such as lifestyle, stress, nutrition, and antibiotic use. A 2021 study showed “how little of the microbiome is predetermined by our genes and therefore how much is modifiable by diet,” according to researcher Sarah Berry.
In this guide, we will cover four proven strategies for improving your gut health. We will talk about some exciting research that will show you how to 1.) breathe, 2.) move, 3.) exercise, and 4.) sleep better to create long-term, sustainable changes to your microbiome and in turn, your overall health and wellness.
Let’s get started …
Download the PDF Version of This Gut Health Guide Here
Breathing
You know that feeling you get when you’re stuck in traffic and late for a meeting? Or somebody cuts you off then has the audacity to honk at you?
These types of stressful events cause emotional responses like anger or fear, which prompt an immediate physical reaction within your body: your heart beats faster, your breathing gets quicker, and your stomach tenses up.
This “fight or flight” response causes blood to move from your gut to the larger muscles, which hampers digestion, weakens your immune system, and increases inflammation.
The changes may not last long, and in the short term they aren’t harmful and may even be helpful in certain situations. But when they happen repeatedly, over time they can cause dysbiosis (when your gut bacteria are out of whack).
The good news is, you can learn to recognize and turn off these automatic responses through deep breathing.
Before you dispel this as New Age mumbo jumbo, here’s some science to quell your skepticism.
According to the University of Michigan Health System:
For those suffering from GI symptoms, diaphragmatic breathing offers specific benefits: Activating the diaphragm creates a gentle massaging action felt by internal organs like the intestines and stomach, which can reduce abdominal pain, urgency, bloating and constipation. While diaphragmatic breathing, you are facilitating the activation of the parasympathetic system, which can be thought of as the relaxation response of the body or the “rest and digest” state.
Deep breathing has additional benefits, including:
- Reducing anxiety and stress.
- Improving your mood and sense of well-being.
- Support your respiratory, cardiovascular, cardiorespiratory and autonomic nervous systems.
- May help lower your perception of pain.
- Boost brain function and performance.
Action Steps:
- Read this primer on how to breathe better.
- Practice deep breathing each day. Start with just 1-5 minutes then work your way up from there (I personally aim for 10-30 minutes each day, spread out over 2-3 sessions depending on the day). There are many different deep breathing techniques (progressive muscle relaxation, mindfulness meditation, yoga, tai chi, qi gong, repetitive prayer, guided imagery, the Wim Hoff Method, to name a few).
Eating
Eating for better gut health is a highly individual affair.
In this section, we’ll cover some different dietary approaches that may be beneficial for those GI issues.
First, it’s important to talk to a specialist if you’re having digestive issues to make sure it’s not something more serious. I also highly recommend getting tested for food allergies and getting a gut intelligence test. These two tests will tell you exactly what foods you should and shouldn’t be eating, based on your unique physiology.
Now let’s unpack a few dietary approaches that may (or may not) help improve your gut health.
The FODMAP Diet
FODMAPs (fermentable oligo-, di-, mono-saccharides and polyols) are a collection of short-chain carbohydrates (sugars) that aren’t absorbed properly in the gut, which can trigger symptoms in people with Irritable Bowel Syndrome (IBS) and other gut disorders.
These substances include lactose, fructose, fructans, galactans, and polyalcohols (sorbitol, mannitol, maltitol, xylitol, and isomalt).
Clinical trials suggest that most patients with IBS report a reduction in symptoms from following a low-FODMAP diet.
Also, people with Non-Celiac Gluten Sensitivity (NCGS) seem to benefit from a low-FODMAPs diet and often experience a reduction in gastrointestinal symptoms.
But despite the demonstrated beneficial effects, low-FODMAPs diet have generated some concerns, namely:
- IBS patients have been shown to have a dysbiotic microbiota, which might predispose them to additional pathological dysbiosis (a gut that’s out of balance that can lead to other health issues).
- In one clinical trial, microbiota of IBS patients submitted to 4-week dietary intervention was compared with that of an IBS patient with a habitual diet. The authors demonstrated a reduction in concentration and proportion of Bifidobacteria after the carbohydrate restriction.
- Non-Celiac Gluten Sensitivity (NCGS) patients on the low FODMAP diet experienced a reduction of beneficial Bifidobacteriaceae and an increase of disease-promoting Lachnospiraceae were observed in their gut microbiota.
Taking probiotics might help offset some of this. According to this 2019 study:
Supplementation of the diet with probiotics could help in maintaining the beneficial component of gut microbiota, especially considering the inverse correlation between Bifidobacteria and the symptomatology of IBS.
The Impact of Ketogenic Diets on Gut Health
Low carbohydrate diets like keto, Paleo, and Atkins focus on drastically reduced carbohydrate intake in favor of fats and protein.
More research is needed on the long-term effects of these diets on gut health. Here’s what we know so far, based the current body of evidence:
- A few human and animal studies have shown different results demonstrating positive effects on reshaping bacterial architecture and gut biological functions, while others reporting negative effects as a lowered diversity and an increased amount of pro-inflammatory bacteria.
- According to several different studies, better strategies are needed to maximize the benefit of ketogenic diets. Here’s what they recommend:
- Introduce the use of whey and plant proteins (i.e., pea protein).
- Reduce the intake of animal protein.
- Implement fermented food and beverages (yogurt, water and milk kefir, kimchi, fermented vegetables).
- Introduce prebiotics and probiotics.
- Reduce omega 3 to omega 6 fatty acids ratio (increase omega 3 while decreasing omega 6).
- Introduce an accurate quantity and quality of unsaturated fatty acids.
- Avoid artificial sweeteners and processed foods.
- Test your microbiome if needed (analysis of 16S rRNA to identify biodiversity and richness).
Gluten Free Diets and Gut Health: What We Know So Far
What about a gluten free diet? It’s a low-carb world, and many people are pushing grains off their plate in an effort to control their waistline and improve GI symptoms.
Gluten-free diets are essential for people with celiac disease and other medical conditions that are negatively affected by gluten.
But for most people, gluten is unjustifiably vilified.
A 2019 meta analysis published in the scientific journal Nutrients reported that in patients with cardiovascular disease, after two years on a gluten-free diet, the “imbalance of duodenal mucosal microbiota were not completely restored with a worsening in the reduction of bacterial richness.”
And while some potentially pathogenic bacteria such as E coli and Staphylococcus may decrease on a gluten free diet, levels of beneficial species as Bifidobacterium and Lactobacillus also remain low.
Anti-nutrients: Good or Bad?
Anti-nutrients are natural substances found in certain plant- and animal-based foods that can block the absorption of nutrients. A common refrain you hear from people who swear off grains is that anti-nutrients are terrible for you and cause all types of issues.
That may not be the case though.
According to the Harvard School of Public Health:
- The pros and cons of anti-nutrients on long-term human health is an area of active research.
- Though certain foods may contain residual amounts of anti-nutrients after processing and cooking, the health benefits of eating these foods outweigh any potential negative nutritional effects.
- Eating a variety of nutritious foods daily and avoiding eating large amounts of a single food at one meal can help to offset minor losses in nutrient absorption caused by anti-nutrients.
- Many anti-nutrients have antioxidant and anticancer actions, so avoiding them entirely is not recommended.
Why Most People Should Not Give Up Grains
Based on the current body of evidence, whole grains have some unique digestive health properties that make them a valuable addition to the diet for most people. The pros outweigh the cons.
Teresa Fung, adjunct professor in the Department of Nutrition at the Harvard T.H. Chan School of Public Health, says “The main benefit of whole cereal grains, such as wheat, oats, and barley, is in the fiber. Cereal fiber is different from vegetable fiber or bean fiber.”
A reduced risk of colon cancer has been linked to fiber from grains, but not necessarily fiber from other sources, such as fruits and vegetables, she says.
Whole grains have other health benefits as well. They lower cholesterol levels and reduce chronic inflammation, which has been linked to cancer and heart disease. Reducing chronic inflammation inside the body may also help to control blood pressure.
A 2016 study published in the journal Circulation found that people who ate at least four servings of whole grains each day had a 22% lower risk of death from any cause during the study period, compared with people who didn’t eat as much. The study’s authors also found a lower risk of cardiovascular disease and cancer associated with diets rich in whole grains.
How Whole Grains Affect Your Microbiome
Whole grains break down slowly during digestion, which helps to keep blood sugar levels on an even keel. Similarly, some studies have linked whole grains with a lower risk of getting diabetes.
The fiber in whole grains acts as a prebiotic, which is a substance that helps to feed, grow, and sustain healthy bacteria in your intestines.
One study found that “whole grains, including oats, constitute important sources of nutrients for the gut microbiota and contribute to a healthy gut microbiome.”
Another study published in 2019 in the journal Frontiers in Nutrition showed “Increasing cereal fiber consumption should be encouraged for overall good health and for gut microbiota diversity.
Action Steps:
Cleveland Clinic Gastroenterologist Christine Lee, MD, shares six tips to improve your gut health and digestion naturally.
- Eat five to seven servings of fruits and vegetables a day. Fill your plate with the colors of the rainbow, from red to dark green. Stock up on canned and frozen veggies for convenience, but also be sure to include lots of fresh produce into your meals. Try to add a few veggies with each meal.
- Choose whole grains more often. Look for and choose packages that say “whole grains” more often than white or processed bread or other grains. Then also check the amount of fiber the product contains. Try to choose items with at least 3 grams of dietary fiber per serving for the most benefit.
- If you eat meat, limit the amount of beef, pork, lamb and processed meats you eat. Choose poultry or fish more frequently than red meat and limit all processed meats, like salami, bacon and hotdogs. Smaller portions of meat (1-4 oz.), consumed less often, are also beneficial. Most people don’t need to consume more than 6-8 ounces of meat every day. Try replacing meat with some beans or other plant-based protein for more fiber. One half cup of beans provides the same amount of protein as in 1 ounce of meat.
- Experiment with healthier cooking options. Opt for steaming, poaching, stewing, microwaving, braising and boiling over grilling and frying. And don’t forget – it’s important to make sure your meat gets cooked thoroughly before eating it to reduce other digestive health risks, such as salmonella (author’s note: I spent a day in the hospital after getting salmonella … trust me when I say you don’t want to experience it).
- Consume foods with probiotics. Probiotics are healthy bacteria that help fight off the bad bacteria in your gut. They also produce healthy substances that provide nourishment for your gut. Good sources of probiotics include fermented foods like yogurt, kefir, kimchee, raw apple cider vinegar, onion, garlic and sauerkraut. If those foods don’t suit your fancy, then a probiotic supplement may help.
- Limit foods that have added sugars and animal fats. These foods can produce harmful chemicals in your GI tract and cause major damage over time. Read ingredient labels for sources of added sugars – they can be tricky!
Sleeping
There’s a direct link between sleep disturbances and gut health.
Just as you can influence your waking routine, scientists have determined poor night-time practices and an unhealthy diet can change your gut flora and impact your risk of insomnia.
There are several theories on how your gut microbes might affect sleep:
- The Gut-Brain Axis
The connection between our brain and our digestive system is a complex system connected by the vagus nerve. Key signals can be passed between these two, such as when we’re hungry, stressed, or even our emotional state.
If your gut microbiome shows signs of gut dysbiosis, leading to leaky gut syndrome, it’s possible neuroinflammatory metabolites may be traveling up the vagus nerve and penetrating the brain. These metabolites have been shown to influence our stress response, impacting our heart rate and disrupting sleep structure patterns.
- Hormone Regulation:
Many microbes within our gut microbiome produce serotonin, a key biochemical that regulates our mood. Serotonin is also a precursor for melatonin, another hormone essential to our light-dark cycle that eases us to sleep. If the gut microbiome isn’t producing it’s fair share of serotonin, this hormone flow may cease to a trickle and change standard sleep patterns.
This theory has also been supported by the number of people suffering from mood disorders like depression who also report additional issues with sleep. Researchers from the University of Tsukuba in Japan said, “Changing which microbes are in the gut by altering diet has the potential to help those who have trouble sleeping.”
- Immune System:
Scientists say our gut houses upwards of 70% of our immune system. When we’re at our optimal health, this “immune organ” works in peak performance like an efficient fighting machine. However, when our body is under long-term assault from toxic substances, invading bacteria, or injury, our immune system can interrupt normal processes and change how well we regulate our sleep cycle.
When the gut ecosystem becomes imbalanced, it can cause an immune reaction that permeates through the digestive lining and penetrates peripheral tissues. If this immune response reaches organs such as the lungs, the inflammatory response can impact breathing at night and increase the likelihood of disorders like sleep apnea.
Action Steps:
- Improve your diet by following the Action Steps in the Eating section above.
- Try a prebiotic / probiotic / digestive enzyme supplement.
- Go to bed and wake up at the same time every day. Try going to bed 20-30 minutes earlier than normal each night. Dr. Meeta Singh, a sleep disorder expert at Henry Ford Sleep Disorders Center says “If you increase your time in bed by even 15 – 20 minutes, you will notice a difference.”
- Don’t eat or drink caffeine in the afternoon. Caffeine can disrupt your sleep. Cut it out after 3 p.m.
- Don’t drink too much alcohol. 1 or 2 drinks a night should be your limit. Any more and your sleep will suffer.
- Keep your room as dark and quiet as possible. I have two young kids, so I know “quiet” is relative for many of us. But a room darkening shade and/or a sleep mask is a great investment if you don’t have them. And to drown out those loud kids, pets, partners, use ear plugs.
- Invest in a white noise machine and ear plugs if needed (check out the links for the ones I use). The Lectrofan white noise machine is the loudest and best white noise machine I’ve used … we have four of them in our house!
- Cut out screen time while in bed. Watch TV, check your phone, or dabble on your tablet outside of the bedroom. Studies show technology in the bedroom negatively impacts sleep.
- Spend 15-30 minutes winding down. Read, do yoga, stretch, foam roll, or meditate to wind down before bed. People who do sleep better.
- Invest in a good pillow and mattress. Think about how much time you spend in bed. A good mattress will probably set you back $1000+, but upgrading your pillow is a super easy sleep hack. I recommend the Coop Home Goods Pillow and body pillow. They’re highly rated on Amazon, hypoallergenic, and you can adjust the amount of memory foam inside to your liking.
- Use a sleep tracker. There are many sleep tracking products on the market now. I have used both the FitBit Charge 2 and Charge 3 with success, as well as the Withings Sleep Mat. All are $150 or less. I’ve heard good things about the Oura Ring too, but it’s a bit more expensive.
Moving
Studies suggest that exercise can:
- Enhance the number of beneficial microbial species
- Enrich the microflora diversity
- Improve the development of commensal bacteria.
Microflora diversity is indispensable to homeostasis and normal gut physiology and contributes to efficient signaling along the aforementioned brain-gut axis.
Exercise also improves the Bacteroidetes-Firmicutes ratio, which may contribute to reducing weight and gastrointestinal disorders, stimulate the proliferation of bacteria which can modulate mucosal immunity and improve barrier functions, and stimulate bacteria capable of producing substances that protect against gastrointestinal disorders and colon cancer.
Here are some tips to improve your gut health with exercise …
Action Steps:
- Schedule a little exercise every day. Add a recurring event on your calendar for 5-15 minutes of exercise every day. 5 minutes may not seem like enough, but you will often find that you want to do more when you have the time. And even if you only have time for 5 minutes, it’ll help you create a habit, which is imperative to long-term success.
- Find some types of exercise you don’t hate. You’ll be more likely to stick with something you enjoy. So try different types of workouts until you find a couple you like doing.
- Switch things up for best results. You need to constantly push your body outside of its comfort zone to create adaptation. The point of diminishing returns happens when you do the same thing for too long and it yields less and less desirable results relative to the work put in. Constantly seek out and try new ways of moving.
- Don’t sit for more than 20 minutes at a time. If you spend a lot of time sitting, changing that habit is one of the best things you can do for your overall health (and particularly your gut health). Stand up and go for a 5-minute walk around your house, stretch, dance, do a few yoga poses. Try “walking meetings” whenever possible. Here are a few of my favorite exercises I do in between my daily tasks.
Pure Food DIGEST is our new, soon-to-be released, 
Cooking everyday. I know that if I get takeout or go to a restaurant then I’m usually not going to eat as healthy. So I try to only eat out about once a week and the rest of the days I make time to cook for myself and my family. I schedule time on my calendar from 5-6ish every day to cook dinner and prepare lunches for everyone for the next day.
