Adapted from episode 53 of The Perfect Stool podcast and edited for readability.
This blog is geared towards people who are interested in maintaining their gut health, learning how their gut health impacts their overall health or who only have minor or occasional gut issues. This is not one of my advanced level topics for people who’ve got longstanding gut issues and who make a minor career of studying gut health and the gut microbiome. So, for my longtime readers, please be patient as I spell things out in detail, and for new folks, welcome!
If you’re a person who generally has had good gut health, and by that I mean good digestion, regular stool, and you only have indigestion or bloating or feel bad occasionally when you overeat, eat a lot of junk food, or eat something that seems to disagree with you, then you may be interested in maintaining your good gut health or hearing about easy remedies for basic issues. Or maybe you’re a person who seems to have good gut health but has other issues, like autoimmune disease, mental health challenges, headaches or skin issues. I’m going to talk a little about how all this relates to your gut.
Could my gut be at the root of my autoimmune or mental health issues?
The gut is host to both good or commensal and bad or pathogenic bacteria that generally stay in balance, because the good ones or the general diversity of good ones keep the bad ones in check. Now since 70% of our immune system is housed in our gut, an overgrowth of bad bacteria can lead to an elevated immune response, which is what inflammation is. Inflammation can cause fatigue, depression, brain fog, migraines, autoimmune disease, acne and other skin issues, among other symptoms. And the gut-brain connection goes both ways: just as an unhealthy gut can affect the brain, mental stress can upset the gut. I talk a lot more about that in episode #30, Food for Thought: Mental Health and the Gut.
Given the food that we eat, at least in the US, our stress levels and the medical system we have, today more people are likely to have an imbalanced gut microbiome than not. Antibiotic overuse, overuse of proton pump inhibitors (acid-reducing medications), higher intake of processed foods and added sugar, stressful lives and jobs, and a more sedentary lifestyle all contribute to gut health issues. Most people associate bloating or acid reflux with the gut, but you might not make the connection between gut health and fatigue or depression, but the reality is the gut is absolutely central to our entire well-being, with a connection to both the brain and nervous system, so if you’re feeling off mentally, it may be time to look downwards, not upwards.
How does diet impact your gut?
Diet is going to be the single most important factor in restoring or maintaining a healthy gut and a healthy body overall. Nothing will move the needle as much as what you’re eating day in, day out. I had a client who came to me with what she thought was irritable bowel syndrome or IBS, as well as to lose weight. When we moved her to a low carb, anti-inflammatory diet (which essentially meant gluten-free and sugar-free in her case) and got her blood sugar into balance, all the IBS symptoms disappeared. So step one if you’re just a little off is eliminating or starkly reducing processed food, sugar and for a time, gluten. There are so many good quality gluten-free options now that many people find it doable and worth it to be mostly or completely gluten-free so they just feel better. You may not necessarily need to eliminate gluten for good, but it’s good to give your gut a break for a month or so and then retest eating it a couple days in a row, 2-3 times/day before deciding how you do with it. I personally don’t do well with gluten and I’m kind of happy about that because most of the food with gluten in it isn’t really healthy to begin with, so it gives me an excuse to opt out of all those empty carb calories. I did a whole podcast on gluten, it’s episode 21.
How does sugar impact your gut health?
In terms of sugar, your best bet is to find healthy, sugar-free alternatives that you like, of which there are tons these days like stevia*, monk fruit extract*, and if they don’t bother your gut, sugar alcohols like erythritol*, xylitol*or allulose* (also available in liquid* form). Use those for more regular consumption when you want something sweet and limit desserts with actual sugar to occasional, maximum once or twice a week treats, if absolutely necessary. Sugar causes inflammation and feeds yeast and unhealthy bacteria, so eating daily dessert can ultimately lead to gut health issues, especially if that is on top of other processed carbs like bread, bagels, pancakes, tortillas, pasta, etc.
But if you love to bake like I do, the sugar alcohols substitute well for regular sugar and taste exactly like sugar with no bitter aftertaste. Xylitol substitutes 1:1 but does cause loose stool for some people and erythritol and allulose are less sweet than sugar, so about 1 cup of each is equal to ¾ cup sugar, and they lead to less or no digestive upset for most people. We don’t digest them and neither does our gut bacteria so they just pass through us harmlessly. And I’ve found with both myself and my clients that you can lose weight and lower blood sugar even while consuming these safer sugar alternatives, which is not the case for artificial sweeteners like aspartame and acesulfame potassium which are found in diet sodas.
In addition, if you sense that you have issues with the lactose in dairy, like gas, bloating or soft stool, I’d suggest trying lactose digestant tablets* or dairy digestant tablets with soft cheeses and milk, or large quantities of any kind of cheese. Some folks are also sensitive to casein – I personally found that eliminating all dairy got rid of my acid reflux, so for some people, that’s a necessary step to having consistently good gut health.
Does processed food negatively impact your gut?
One more word about processed food – because a lot of people fancy they don’t eat a lot of it – if it comes in a box, can or bag, it’s processed food. That being said, there are totally crappy, non-organic, additive-laden foods full of unpronounceable ingredients, and there are organic processed foods with few ingredients that independently would be considered healthy. So if you’re choosing bread, pasta, ice cream, chips, etc. obviously there are better and worse choices and you don’t need to be a rocket scientist to figure out which those are. But if you need help figuring it out, Environmental Working Group’s Food Scores database can help you determine if there are questionable ingredients in your food, and which are the most problematic ingredients and foods overall.
Speaking of organic food, eating organic is important for many reasons related to gut health, including that organic foods contain fewer pesticides, like glyphosate, which is designed to kill bacteria. They also contain fewer heavy metals, and include more healthy fats, with organic meats and dairy containing 50% more anti-inflammatory omega-3 fatty acids than conventionally-produced products. Organic foods also come without antibiotics and synthetic hormones, and contain more antioxidants. While it would be ideal to consume all organic products, this can be expensive. So if you need to prioritize, check out Environmental Working Group’s Dirty Dozen produce list, which includes strawberries, apples and grapes, which have been found to contain the highest amount of pesticide residues and their Clean 15 list, or the least polluted produce. It is also recommended to buy organic and even better, pasture-raised eggs, dairy and meat whenever possible.
Eating farm fresh and organic foods starts from the bottom up. Literally. For years, chemical fertilizers, pesticides and fungicides have destroyed the soil microbiota in which conventional crops are grown, which are essential to plant health and nutrient content. Fortunately, microbial species are beginning to be reintroduced into soil to help repair damage, but until our farming system changes, organic, pastured and local where you know your farmer foods are a good place to find these chemical-free products. For some people, just making the switch to organic foods may be all you need to resolve not just gut health but overall health issues.
Which diet is best for my gut health?
In terms of overall eating patterns, my personal bias based on all I’ve read and heard is anything from a lower carb Mediterranean diet, which would be higher in seafood and include complex carbs like beans, lentils and whole grains and lots of fresh fruits and vegetables, to a paleo diet, which is grain-free and totally processed food free, for the average person. I am generally not in favor of vegetarian or vegan diets, other than perhaps a vegetarian diet with some inclusion of seafood for people of blood type A, who tend to do better with that type of diet. If for ethical reasons you need to follow a vegan diet, you’ll likely need to supplement with l-carnitine* and B12* at minimum, but in the long term, this kind of diet, unless it’s very carefully monitored, can lead to protein deficiencies that can ultimately break down the gut lining and lead to a host of other random bodily problems that occur when the body can’t do everything that it does with amino acids, the building blocks of proteins. I’ve started using a new test called the ION profile with 40 amino acids with some clients and for my vegetarian clients, I have seen many specific amino acid deficiencies, each carrying potential negative health consequences. But if you’re doing well on a vegetarian diet and you’ve been doing it long-term, just ignore me – there are plenty of advocates out there for plant-based diets.
Does coffee cause gut issues?
In addition to food, caffeine and alcohol are common gut irritants. In general, coffee has actually been shown to have numerous health benefits. It’s full of antioxidants and micronutrients and studies have shown it to promote longevity, lower rates of heart disease, cancer, and a whole bunch of other benefits. Coffee has also been shown to boost energy, fight depression, lower risks of certain gastrointestinal diseases, and even prevent diabetes. However, like most things, coffee comes with its own set of cons. Coffee is infamous for its laxative effect, due to the release of gastrin, which stimulates movement in the digestive tract. The same adrenaline triggered by coffee that gives people energy can also lead to anxiety and nervousness. Studies have shown that coffee can worsen GERD, or gastroesophageal reflux disease, also known as acid reflux, and cause nausea, vomiting and diarrhea. Pregnant women and children are discouraged from consuming large amounts of coffee – up to 400 mg of caffeine a day is considered healthy for the average adult, which is around 4 cups of brewed coffee. People with certain gut health issues like IBS, SIBO and IBD should also be more careful. Quitting coffee can support better sleep, whiten teeth, improve mood and increase weight loss, as many people add lots of sugar to make coffee palatable. If you’re overwhelmed by the thought of giving up your daily coffee fix, you should be encouraged knowing that once your gut heals, you can try to reintroduce it in moderation. In the meantime, caffeinated teas like green and black tea, along with yerba mate can serve as substitutes.
How does alcohol impact gut health?
Alcohol is another popular yet problematic beverage for gut health. A review of the peer-reviewed literature on alcohol and the gut found that alcohol can cause both dysbiosis, or an imbalance in bacteria and fungi in the gut, as well as bacterial overgrowth, also known as SIBO or small intestine bacterial overgrowth, the cause of 70-80% of IBS or irritable bowel syndrome. This can lead to symptoms like bloating, soft stool or diarrhea, constipation, loss of appetite, uncomfortable fullness after eating, nausea, unintentional weight loss and nutrient deficiencies. Alcohol-induced bacterial overgrowth also leads to inflammation and contributes to intestinal permeability. Intestinal permeability, also known as leaky gut, is when the tight junctions in the intestinal wall that allow nutrients out and keep toxins, microbes and undigested food in, open up too wide and allow some of those last three items out. This means that undigested food particles can enter the bloodstream, provoking an immune response and causing food sensitivities, and if left long enough, autoimmune disease. Many Americans will be surprised to discover that they are considered heavy drinkers. For men, that means consuming more than 4 drinks on any day or more than 14 drinks per week and for women, that means consuming more than 3 drinks on any day or more than 7 drinks per week. If you’re concerned about your gut health or are beginning to notice symptoms, you should watch your alcohol consumption and the effect it might be having on your body.
Like coffee, not all alcohol is toxic, or better said, alcohol can have some benefits. For one, red wine has been linked with health benefits because of the antioxidants called polyphenols it contains. One of them, resveratrol, has been associated with lowering the risk of heart disease. However, research is mixed, with other studies not finding any significant relationship between resveratrol and lower chances of heart disease. The key is to drink in moderation, and for pregnant women, people on certain medications, those with a liver disease or a history of alcoholism, to not drink at all. There are also ways to consume alcohol in a more responsible manner. It is unwise to drink alcohol on an empty stomach, and people should always make sure they are hydrating with water between drinks or drinking a glass of water alongside every drink.
How does stress impact my gut?
Lifestyle and stress are also really important for your gut health. Digestion disorders often go hand and hand with mood disorders. One study of 23 healthy, undergraduate students took saliva and fecal samples at the beginning and end of a semester. As stress increased throughout the semester, certain healthy bacteria decreased. Both depression and stress weaken the immune system, which in turn weakens the gut barrier which ultimately leads to leaky gut. Certain lifestyle changes like reducing work hours, taking regular vacations, practices like meditation, EFT, yoga, tai chi or other such modalities and regular exercise can help combat stress levels, as can seeking therapy or life coaching to deal with bigger issues.
Another lifestyle factor that can impact gut health is exercise. Studies link exercise with enriched gut microflora diversity, which is touted as the most important factor in all the recent studies on various aspects of health and the gut microbiome. Some of the specific preventative health benefits of exercise on the gut include its ability to lower chances of colon cancer and inflammatory bowel disease, that is, Crohn’s and colitis.
Will antibiotics ruin my gut health?
Speaking of prevention, let me return to what I believe is one of the principal driving factors in poor gut health: antibiotics. Obviously antibiotics are a very effective modern medicine that can save lives, but these days, doctors often overprescribe these drugs for even the smallest issues. Common conditions for which you may be prescribed antibiotics include ear infections, urinary tract infections, throat infections and sinus infections, many of which are in fact viral in nature, and antibiotics do not kill viruses. So if you have a cold or the flu, don’t go to your doctor looking for a prescription. Antibiotics are also not beneficial in treating some ear infections and sinus infections, so be sure to ask your doctor to culture what’s in your sinuses or ears before prescribing anything.
Overuse of antibiotics is a problem because while antibiotics kill off bad bacteria, they can also kill off good bacteria. This weakens your body’s ability to fight off infections, and can lead to overgrowth of more harmful bacteria like E. coli and C. difficile or just lead to general dysbiosis, like an overgrowth of proteobacteria, streptococcus or other clostridia species beyond C diff. Antibiotics come with a whole host of side effects, like diarrhea, yeast infections, vomiting and constipation. Just one week of antibiotics can change the makeup of your gut microbiota for a whole year. So the first thing you can do is always question your doctor before taking antibiotics. Are these absolutely necessary? Is this the narrowest spectrum antibiotic I can take for this issue? Could we wait and see a few days or run a culture before I start them or should I stop them if the culture comes back negative? Could I take a shorter course of antibiotics? On a side note, I think that many of my health issues started after taking two 10-day courses of Cipro in one year for urinary tract infections. I later learned that the usual course of Cipro for UTIs is only 3 days.
What can I do if I have to take antibiotics to protect my gut microbiome?
If avoiding antibiotics is not an option, there are several measures one can take to promote a healthy gut. Maintaining a healthy diet full of fermented foods, high fiber foods like nuts and berries, and prebiotic foods is essential. Avoiding sugar, processed white carbs and junk food while taking antibiotics is also important. Taking probiotics both during and after a dose of antibiotics is controversial since a study from 2018 showed that people’s microbiome’s took much longer to recover while using probiotics after taking antibiotics. One alternative you could consider is to take butyrate while on antibiotics, to keep a bacterial phylum called proteobacteria from overgrowing, which is a common result of taking antibiotics. Butyrate is a short chain fatty acid that feeds the cells lining your colon and the best and most palatable formulations are probutyrate* or tributyrin*. 1200-1500 mg/day all at once has worked well for me as I have a tendency towards proteobacteria overgrowth most of the time. You should reduce the quantity of butyrate, however, if you start to get constipated. But if you do experience antibiotic-associated diarrhea, one probiotic that I think is relatively safe is Saccharomyces boulardii, the most studied strain of which is Saccharomyces boulardii CNCM I-745 sold everywhere as Florastor*. In studies, it has been shown to help alleviate antibiotic-associated diarrhea, and it’s a beneficial yeast that also keeps candida in check, so for women it may help to prevent a post-antibiotic yeast infection, which is a common problem for many women. You can take it while on antibiotics too because it’s a yeast, not a bacteria, and won’t be killed by your antibiotics.
Are probiotics beneficial for your gut microbiome?
But for people who have been having gut issues and are not trying to recover their previous gut microbiome but change their current one, probiotics may be warranted as they can help alter your gut microbiome in a positive way or just help maintain a healthy balance of bacteria in your digestive system in the face of the inevitable insults it may experience, as well as improve mood and mental health. In one randomized, double-blind study of patients with clinical depression, taking probiotics for 8 weeks significantly improved the mood of patients compared to ones administered the placebo. One probiotic for general good health that I’m particularly impressed by lately is Seed Synbiotic** (get 15% off your first month with my affiliate discount code PARSONS15), which I started taking about a month and a half ago to good effect. Seed’s scientific advisory board includes some of the big names in microbiome science (think Martin Blaser and Alessio Fasano).
Of course, probiotics can also be found in fermented foods like kefir, yogurt, kimchi and sauerkraut and it’s always best to get your nutrition from food if possible. However, probiotics won’t work to their full effect if you’re just taking them alongside a high simple carbohydrate diet. You need to include lots of healthy prebiotics like complex carbs, beans, legumes, fruits and vegetables that are high in fiber and aren’t easily absorbed in the upper intestine, and therefore make their way down to the colon. That fiber provides food for your healthy bacteria, which then produce short chain fatty acids like butyrate that nourish the gut lining. Some other prebiotic foods include onions, garlic, spinach, oats and you’ll be excited to know, dark chocolate, just to name a few. I did a whole episode on fiber and prebiotics, episode 28.
Can NSAIDs cause ulcers?
Antibiotics aren’t the only common drugs to be more cautious about. NSAIDs or nonsteroidal anti-inflammatory drugs are over-the counter drugs like aspirin, ibuprofen or Advil and naproxen sodium or Aleve. When overused, NSAIDs can cause milder symptoms like nausea and dizziness, while more extreme symptoms such as ulcers and liver failure are rarer but possible. For elderly people and those on certain medications, NSAIDs put them at a higher risk of developing potentially fatal reactions in the stomach and intestines, like bleeding and ulcers. When I was going through sciatica last year, I was in so much pain that I found myself taking as many ibuprofen as my doctor allowed me, which was I think 600 mg 3 times a day for several weeks. I started having consistent pain in my stomach after taking them and I knew I had to stop or I’d end up with an ulcer. So do be careful, especially if you start having stomach pain or other symptoms of an ulcer like nausea, vomiting, bloating, feeling full easily, weight loss, burping, acid reflux or heartburn while taking NSAIDs, and stop and see your doctor if you do experience those symptoms.
How does sleep impact gut health?
On another topic, you may be surprised to learn that good sleep is essential to maintaining a happy gut. If you start losing out on sleep, this can increase your stress levels, which can unbalance your cortisol, which can lead to leaky gut and all that follows. Lack of sleep can also lead to GERD, as the hormone our body produces to help us go to sleep, melatonin, also regulates gastrointestinal mobility. If your melatonin levels are off (and by the way, serotonin is a precursor to melatonin, so you may also experience anxiety with your insomnia) you may end up with acid reflux. So be sure to get some full sunlight each day for 15 or 20 minutes without sunscreen to keep those melatonin levels up. And I hate to give this advice because I can’t seem to follow it myself, but you really should avoid eating for 3 hours before bedtime. Eating closer to bedtime can disrupt your sleep and leave less time for your body to do essential detoxification and cleanup tasks in your brain and body while sleeping. This includes autophagy, or recycling of older cells, which only kicks in after 13 hours of fasting and is preventative for cancer and dementia, just to name a couple of conditions.
When should I see a doctor for my gut issues?
Moving from prevention to diagnosis, it’s important to recognize when you may be starting to have some gut health issues that could get worse if not addressed. First, let me talk about the difference between healthy bowel movements and more serious gut issues. Signs of a healthy bowel include passing a well-formed, soft but not loose or mushy stool 1-3 times a day and finishing with a clean wipe. This would be a number 3 or 4 on the Bristol Stool Chart. You should be able to pass a bowel movement without pain, and hold onto a bowel movement for a short time once you feel the need to go. Constipation versus diarrhea and urgency sit at opposite ends of the stool spectrum. It’s normal to have occasional bouts of each extreme, but if you experience constipation or diarrhea for weeks or months that doesn’t resolve with diet changes or the addition of fiber like psyllium husk or Sun Fiber, you should start by seeking out a gastroenterologist to see if you have any physical gut problems. You should also seek out your doctor if you find blood in your stool, have foul smelling stools or are experiencing incontinence. These signs could point to inflammatory diarrhea caused by something like C difficile, IBD, or even colon cancer.
Upon meeting with the gastroenterologist, they will likely conduct one or more exams to find the root of the issue. Colonoscopies are performed by inserting a tiny camera into the rectum so the doctor can see the inside of the colon wall and look for inflammation. Endoscopies give the doctor a sense of the rest of the GI tract by inserting an endoscope down the patient’s throat in order to examine the esophagus, stomach and small intestine. To detect for an autoimmune disease caused by a reaction to gluten, celiac testing can also be done, as well as something called a Stool Antigen Test to determine whether you are symptomatic for H. Pylori, which is more accurate than a breath or antibody test. H. pylori may be the issue with GERD or upper GI symptoms like nausea or burping, as well as abdominal pain or burning, especially when your stomach is empty. And an ova and parasites exam, which is not likely to find anything as they rarely do when done from regular doctor’s offices, may be done if you have ongoing diarrhea.
What kind of alternative health practitioners can help with a gut problem my gastroenterologist can’t?
Despite all these methods used to diagnose a patient’s gut problems, often I find that GI doctors are unable to make a diagnosis, or they give you a diagnosis like IBS, which in my opinion isn’t a diagnosis, it’s just a name for a constellation of symptoms that allopathic doctors don’t know how to resolve. If you have a GI doctor that follows current research and developments, you may be lucky enough to get a SIBO or small intestine bacterial overgrowth breath test (the best of which is the trio-smart test) and a prescription for rifaximin (antibiotic that helps resolve SIBO), but for many people this leaves them feeling worse and doesn’t resolve their problems. In these cases, it is useful to look for alternatives to western medicine like a naturopath or someone like myself. I help my clients get functional gut health tests like the GI Map*, which uses DNA testing to test for parasites and bacteria, as well as testing markers of gut organ function, or the Organic Acids Test*, which tests not just for bacterial and fungal overgrowths but also looks at whole body functioning, including neurotransmitters, which can point to why you may be experiencing anxiety or depression, the functioning of your energy production from carbs, fats, and proteins, which can point to the cause of weight loss resistance, markers of high oxalates which can cause not just kidney stones but problems like UTIs, interstitial cystitis, cardiovascular and brain issues; levels of antioxidants and B vitamins, and detoxification markers, which can signal incipient liver issues.
To conclude, just because you haven’t received an official diagnosis doesn’t mean your gut health issues are not worthy of being addressed, because if left alone, gut issues can get much worse. Often, the difference between a good and bad day boils down to simple lifestyle and diet choices. Each of you needs to find the unique combination of choices that works for you. Although the routines we’ve maintained our whole live may be hard to break, after the initial push, healthier practices can easily become your new normal.
If you’re struggling with any type of gut health problem and are ready to get some professional help, you’re welcome to set up a free, 30-minute breakthrough session with me. We’ll talk about what you’ve been going through and I’ll tell you about my gut health coaching 5-appointment program in which I recommend lab tests, educate you on what the results mean and the protocols used by doctors to fix the problems revealed. Or if you’re ready to jump in right away or can just afford one appointment at a time, you can set up an 1-hour consultation with me.
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**I am an affiliate of Seed but do not receive commission on product sales.