Adapted from episode 111 of The Perfect Stool podcast and edited for readability, with Lindsey Parsons, EdD, Gut Health Coach.
If you’ve been struggling with feeling comfortable in your body, weight gain or weight loss resistance, and wondering if maybe your gut health or gut health issues might have something to do with it, beyond the obvious regarding your diet, I wanted to address that today.
Before I go into that, I should mention that before I focused in on gut health, I worked with clients on sustainable weight loss without dieting, because I think it’s really important that any lifestyle changes you make be sustainable in the long-term. I’m not in favor of, nor do I recommend, low-calorie diets, crash or fad diets, because severely restricting your food intake can disrupt normal bodily functions, doesn’t promote sustainable long-term weight loss and can result in muscle loss and a reduction in your basal metabolic rate, which plays a crucial role in calorie burning. And even worse, undereating often causes your body to store calories as fat. It is not recommended for individuals to consume fewer than 1,200 calories per day unless you’re being supervised by a doctor and I’ve often seen people on such low calorie diets that started to lose weight only when they started eating more.
I also rarely recommend long-term extreme diets like carnivore or ketogenic diets, perhaps with the exception of people who have diagnosed type 2 diabetes that’s in need of immediate and extreme attention. And I think that self-acceptance is very important at whatever size your body naturally rests when you’re eating a healthy diet 95% of the time and exercising regularly, getting good sleep, managing and reducing stress and practicing all of the health-supportive behaviors we all hear so much about. And part of that self-acceptance is consuming media that highlights and supports diverse body types and sizes and reducing exposure to media that exclusively promotes a certain body type or filtered or altered images of unrealistic bodies. And I also think it’s very important, especially if you have any disordered eating behaviors like binge eating, emotional eating, anorexia or bulemia, to address the mental health component of weight gain, especially if you have a high level of Adverse Childhood Events, known as ACEs, that are highly correlated with obesity. If that’s part of your history, I’d recommend looking into trauma-focused therapies, which include modalities like somatic experiencing, AEDP, EMDR and neurotherapy. If you’ve gone through therapy but only traditional CBT-type talk therapy or Cognitive Brain Training, I’d recommend you look into these other modalities in conjunction with whatever other interventions you’re considering.
That being said, research over the last 20+ years into gut bacteria has shed light on its pivotal role in regulating weight and weight loss. So you may have heard about early studies suggesting that a key marker in the microbiome of obese individuals was an excess of gram positive bacteria in the Firmicutes phylum, in particular as it related to gram-negative Bacteroidetes and a high Firmicutes to Bacteroidetes ratio, the two principal phyla of bacteria in the human microbiome. However, these results have been called into question in a resequencing of the DNA from 9 of those previous studies. It was found that methodological differences in sample processing and DNA sequence analysis, interpretive bias and confounding factors that weren’t accounted for such as exercise and altitude, which have been shown to impact the gut microbiota, may have been responsible for these results. Further studies in animals and then in humans over the course of 5 days have shown that the composition of the gut microbiota can change rapidly when subjects are fed different diets. In particular, one study showed that a 5-day animal-based diet increased the abundance of bile-tolerant organisms from the genuses Alistipes, Bilphila and Bacteroides and decreased the level of Firmicutes from the genus Roseburia as well as the species Eubacterium rectale and Ruminococcus bromine, which metabolize dietary plant polysaccharides.
What I believe is a more important factor to consider with regard to weight loss resistance and/or weight gain is lipopolysaccride or LPS, an endotoxin that creates inflammation in the body and is released by and is a component of the cell wall of gram negative bacteria. Studies have shown that elevated blood levels of LPS are associated with prediabetes, diabetes and obesity, while additional studies have shown that translocated gut bacteria are the origin of that LPS. One of the reasons beyond diet that many people end up with elevated levels of gram negative bacteria, in particular from the Proteobacteria phylum, is use of oral antibiotics. As I’ve described in previous podcasts, antibiotics reduce the body’s ability to produce butyrate, the primary food for the cells lining your colon, which comes form the fermentation of fiber in the colon by butyrate-producing bacteria primarily from the Clostridium cluster of the Firmicutes phylum. In animal experiments, 3 days of oral antibiotics decimated the gut’s ability to produce butyrate from fiber and increased oxygen levels in the colon, which is an alternate fuel source for these cells lining the colon. This oxygenation of the colon produces a wonderful habitat for gram negative proteobacteria because they are facultative anaerobes, meaning they can exist in the presence of oxygen. This can then lead to a vicious cycle where proteobacteria continue to dominate, and the colon fails to recover its preferred hypoxic, or oxygen-free state, because of lack of butyrate, and butyrate-producing bacteria that are obligate anaerobes are wiped out. What’s more, a high-sugar diet in rats has been shown to increase proteobacteria, one of the reasons for which I recommend that people eat a super healthy, sugar and flour-free diet while on antibiotics.
The domination of proteobacteria then creates a vicious cycle of high LPS in the body, promoting inflammation, blood sugar dysregulation and increased weight gain. Likely because of this phenomenon, probiotic bacteria that restore the balance of butyrate producers and also mucin-degraders like Akkermansia muciniphila, which reside in the mucous lining of a healthy colon and live in symbiosis with the butyrate producers, have been shown to decrease hemoglobin A1C, a longer-term marker of blood sugar. The first product on the market of this kind, which contains 3 strains of anaerobic, butyrate-producing bacteria, was Pendulum’s Glucose Control*, which has the strains Clostridium butyricum, Clostridium beijerinckii, Anaerobutyricum hallii and Akkermansia muciniphila. While it’s not inexpensive (a monthly supply will run you $177/month via my Fullscript Dispensary, which includes the discount I give my followers), the company’s study on it showed a reduction in hemoglobin A1C of 0.6% and a 32.5% reduction in post-pradial glucose spikes after 12 weeks. You can also get just the Akkermansia* and the Clostridium butyricum* in separate products that are more reasonably priced, which I’ll link to in the show notes.
Because SIBO or small intestine bacterial overgrowth can also cause an overgrowth of proteobacteria, with Klebsiella, Citrobacter and E Coli being three of the most common overgrown bacteria in SIBO, I have also struggled with an overgrowth of proteobacteria, since I have post-infectious IBS which is essentially autoimmune SIBO that keeps recurring because of poor small intestine motility. As a result, I’ve tried Butyricum*, Pendulum’s Clostridium butyricum probiotic, and have found that it is very effective in firming up stool, which is a good indication of butyrate-production in my colon, which slows colon motility. I have found, however, that I can only handle ½ capsule a day, as a full capsule lead to downright constipation and sometimes pain and cramping. At ½ capsule it’s a perfect adjunct for keeping me in steadily perfect stool, along with tributyrin supplementation, the preferred form of butyrate for supplements, which I also have found indispensable in the face of a likely lifelong recurrent Hydrogen SIBO issue.
In addition, direct supplementation with butyrate in various forms has been shown in animal studies to positively affect the function and metabolism of fat tissue, increase insulin sensitivity and help with body weight control. For humans, results have varied between individuals, and I personally only recommend butyrate to people who have loose stool or diarrhea, as it will constipate you unless you use it at very small doses. Its success in weight control in animal studies is likely due to its help in turning around the vicious cycle of proteobacteria dominance in the colon and the subsequent release of LPS. Because of its unpleasant taste and odor as well as absorbability, the preferred forms of butyrate are tributryin, which is what I put in my tributyrin supplement Tributyrin-Max, which is 750 mg a capsule of tributryin, or the CyLoc™ form, an alpha dextrin fiber matrix butyric acid complex, used in Probutyrate*, which is only 300 mg a pill if you want a lower dose, which is more appropriate if you’re starting with firm stool or AuRx*, if you want a powder. Both Probutyrate and AuRx are Tesseract products, and you can find all of these in my Fullscript Dispensary at a discount. If you do have firm but incomplete evacuation or a sense that there’s more to go, I’d recommend starting a low dose butyrate supplement like Probutyrate once every 3 days.
Of course, along with taking probiotics or butyrate, I’d recommend increasing fiber intake through 5-9 servings a day of fresh fruits and vegetables, vegetables primarily, including ½ cup of beans, chick peas, peas or lentils on a daily basis to feed the microbes you’re working to restore in your colon.
Another way in which gut health is connected to weight loss resistance is through low stomach acid. Because sufficient stomach acid is necessary for breaking down proteins into amino acids, if you have low stomach acid, you may become deficient in an amino acid called l-carnitine. L-carnitine is found primarily in animal foods, most abundantly in beef and lamb, as well as formed by the body from the essential amino acids lysine and methionine. Because of this, I often find vegetarians and vegans are deficient in l-carnitine as well. L-carnitine is one of two molecules necessary for bringing fatty acids into the Krebs Cycle for production of ATP or energy. The other is vitamin B2 or riboflavin*. While researching for the podcast, I also happened upon a study that showed that riboflavin supplementation at doses of 50 mg or 100 mg a day also increased butyrate production in the colon, coincidentally. So if you’re struggling with weight loss resistance coupled with low energy (which happens when your fats are being stored and not converted into ATP), and you don’t have a blood sugar dysregulation issue indicated by high fasting glucose or high hemoglobin A1C, you may want to check your fatty acid metabolism through an Organic Acids Test* and/or try supplementing with l-carnitine* or acetyl-l-carnitine* to see if it will spark some weight loss. Typical doses are in the range of 3000 mg/day for l-carnitine when there is a deficiency, some of which can be taken in the form of acetyl-l-carnitine* if you’re also struggling with brain fog or poor memory or other signs of low energy in your brain. And a B complex is often also helpful, so a good quality B complex with appropriate amounts and forms of the various B vitamins is the best choice if you’re trying to cover all your bases with fatty acid metabolism. You’ll be wanting to get at least 50 mg of B2 if you have an identified deficiency.
And then on top of that, you could also start a trial of Betaine HCl*, or supplementary stomach acid, to see if that will help you digest protein better. The usual way is by taking 1 pill with meals with animal protein for a couple days, then moving to 2 pills per meal and up to 5 per meal until you feel reflux, warmth or burning in your chest, then you will want to back down to the previous dose.
Then you should looking at causes for low stomach acid. First, maybe your sodium intake is too low. Salt or sodium chloride, is one component of stomach acid. If you eat no processed foods and salt lightly, you’re likely falling short of the goldilocks levels of sodium, which is between something like 500 and 2300 mg/day, although some sources recommend keeping it under 1500 mg/day. And of course it’s better to choose a high quality salt like himalayan pink salt* or Redmond Real Salt* or one of these good quality salts that have trace minerals rather than just regular store-bought salt.
If you have any signs of gastritis, or inflammation of the lining of the stomach, like gnawing, aching or burning or pain in your stomach (and note that’s different from reflux in your esophagus which can be from low stomach acid), nausea, vomiting, a feeling of fullness in your upper abdomen after eating, trouble with acidic foods, or a known history of H. pylori or ulcers, this can also be at the root of low stomach acid. Healing H pylori, or addressing gastritis first may be necessary as you don’t want to add Betaine HCl or digestive enzymes for that matter, to a stomach that’s already inflamed. You can learn more about that in episode 34 called Upper Digestive Issues.
Next, Candida overgrowth in the gut can also be related to weight gain and weight loss resistance, causing sugar cravings and hormonal imbalances. This can come about from overuse of antibiotics as well as a diet high in sugar and simple carbohydrates. If you have a history of heavy antibiotic use, have a white or yellowish coating on your tongue, crave carbs and sugar, have a history of yeast infections, are usually cold, have fungus in your toenails or have brain fog, these are some of the key symptoms pointing to possible a systemic candida infection. While candida is a normal resident of your gut, an overgrowth of this yeast can lead to systemic candidiasis, where it forms hyphae or tails that poke out holes in between cells lining the intestines, giving it entry into the bloodstream. The only reliable way I’ve found to assess candida in the gut is through an Organic Acids Test. The D-arabinitol marker on the Organix, Metabolomix or NutrEval tests by Genova* is the most studied marker of candida, but I’ve also had good results with the Mosaic (formerly known as Great Plains) Organic Acids Test*, which has a marker called Arabinose. You can get some sense of how systemic and entrenched the candida infection is by how high your level is on these markers. The reference range on Arabinose tops out at 29, and for D-arabinitol it tops out at 36, and I’ve seen clients with results in the 300’s, just to give you some sense of how high it can go, although I’d consider anything in the yellow or red on the Organix or above the reference range on the Mosaic OAT to be treatment-worthy.
To combat candida overgrowth and facilitate weight loss, antifungal herbs and fatty acids are usually needed often for as long as 8 months in more severe cases, along with binders like GI Detox* to catch diet off at first and prevent severe Herxiemer reactions, which is when you feel like you have the flu, as you start killing off bacteria and candida with antimicrobials. And then often I’ll add in a biofilm disruptor into the protocol, often in the second round of antimicrobials. And note that I will typically change antimicrobials for each two-month round in order to prevent any resistance to the products. For a lighter case of candida that’s less symptomatic, serum bovine immunoglobulins might be sufficient to reduce levels. After treating candida, you can restore the gut lining by supplying essential building blocks for mucosal lining repair like glutamine and herbs like DGL, marshmallow root, aloe vera and slippery elm and nutrients like zinc l-carnosine*. I usually add the probiotic S boulardii* as well for candida, as it inhibits candida’s adhesion, morphological transition and virulence. Along with that, I recommend a diet free of added sugar, refined grains, dairy, gluten, yeast, white potatoes and for 2 weeks, fruit, after which time all fruit but bananas are okay. I prefer people follow this diet while on antimicrobials for as long as they can, knowing that realistically if it will take 8 months of antimicrobials, they may not be able to persist the whole time on such a strict diet.
If none of the above work for you, one more drastic method for changing your gut microbiome for weight loss may be through fecal microbiota transplantation, or FMT. FMT is the process of using a healthy stool specimen and transplanting it into the gastrointestinal tract of a recipient for the purpose of improved health. This counteracts the dominance of pathogenic bacteria in the intestines, ideally creating permanent changes to the microbiome. FMT from a healthy donor has demonstrated a remarkable 90% success rate in curing the antibiotic-resistant bacterial disease Clostridium difficile (C. diff), which is a prevalent infection that occurs in hospitals in the United States, affecting over 500,000 Americans annually and causing 14,000 deaths a year. The transplantation of stool from a healthy donor introduces protective bacteria, overwhelming pathogenic bacteria and offering a potential cure for illnesses originating from an unhealthy gut microbiome.
Regarding weight loss, I do have to say that results are mixed and more research is needed to fully understand the relationship between FMT and weight loss. In one study involving 41 patients undergoing bariatric surgery in Finland, researchers investigated the effectiveness of FMT for weight loss. The findings from the clinical trial suggest that FMT did not demonstrate significant benefits for weight loss in patients undergoing bariatric surgery, although its known that bariatric surgery alone changes the microbiome. In this particular study, there were no substantial differences in weight loss outcomes between patients who received FMT from a lean donor and those who received an autologous placebo, meaning they had their own stool put back in. While this study did not find evidence supporting the efficacy of FMT in enhancing weight loss in the context of bariatric surgery, it’s important to note that research in this field is ongoing, and results may vary across studies.
Other studies have shown more promising results. For example, one such study investigated the impact of FMT on weight loss in patients with obesity, considering clinical and microbial factors. The researchers compared mixed-donor nonintensive FMT with single-donor intensive FMT. Results indicated that 13.2% of patients in the mixed-donor group achieved a weight loss of at least 10%, whereas no patients in the individual-donor group reached this threshold. Despite engraftment in all patients, there were no sustained differences between the two groups, suggesting that intensive individual-donor FMT did not induce lasting weight loss or microbiome changes compared to non intensive multi-donor FMT. Notably, mixed-donor FMT led to a durable increase in the abundance and diversity of butyrate-producing bacteria, once again pointing at butyrate as a key player in the question of obesity and the microbiome. The study also identified associations between weight loss and specific microbial changes. Higher initial amounts and reduction after FMT of Bacteroides dorei were linked to overall weight loss, while a weight loss of 10% or more correlated with increased amounts of butyrate-producing bacteria, including Anaerostipes hadrus, Collinsella tanakaei, and Roseburia hominis.
These findings, suggesting differential impacts of FMT regimens on microbial composition and weight loss, highlight the value of personalized microbial-based therapies for obesity based on donor and recipient selection. This personalization could include matching donors with specific microbial profiles to recipients to enhance the success of FMT interventions, although the evidence seems to point more and more to butyrate and butyrate-producing bacteria as a key mover in weight loss. Additionally, the frequency and duration of FMT sessions, as well as associations with specific bacterial species, could be factors influencing the weight loss response. While these findings provide valuable insights, further research is needed to establish broader guidelines for the application of FMT in weight loss interventions.
Another area in which the gut may be affecting weight loss is around gluten sensitivity. One randomized clinical trial aimed to investigate the effects of a gluten-free diet on components of metabolic syndrome. The results indicated that the gluten-free diet led to a significant reduction in waist circumference and improved glycemic control and triglyceride levels compared to the control diet. The findings suggest that a short-term gluten free diet can positively impact some key features of metabolic syndrome, specifically reducing abdominal fat, improving blood glucose levels, and lowering serum triglycerides.
Many individuals without metabolic syndrome may have slight gluten sensitivity, not to be confused with Celiac disease, and this gluten sensitivity could lead to weight gain or hinder weight loss. Leptin, a crucial hormone in signaling feelings of fullness to the brain, plays a key role in regulating hunger and satiety to maintain a healthy body weight. However, individuals classified as overweight or obese often experience leptin resistance. This condition, characterized by high leptin levels without a corresponding cellular response to satiety signals, hinders the body’s ability to manage hunger effectively. A study conducted by Swedish and Danish researchers and published in the December 2005 issue of “BMC Endocrine Disorders” suggests that grains, particularly those containing gluten, may contribute to the development of leptin resistance, potentially leading to weight gain and obesity.
Whatever the mechanism is, I can tell you one thing from my own personal experience. I eliminated gluten because it’s known to be a risk factor for autoimmune disease, and I was trying to reverse my Hashimoto’s thyroiditis. Anyone with an autoimmune disease is recommended to stop eating gluten, because of its role in creating a leaky gut (which also predisposes you to LPS leaking out). As a result of being strictly gluten-free, I avoided so many breads, cookies, cakes, pies, etc. that I would have otherwise eaten, thereby making it much easier to avoid sugar, which of course is related to weight gain. And when I knew I’d be going somewhere with desserts and would feel deprived, I’d make my own almond flour muffins with xylitol as a sugar substitute and eat that instead. And I did, by the way, successfully reverse my Hashimoto’s. I have had normal antibodies for like 3 years now and still have optimal TSH levels and have never had to take thyroid hormones, since my diagnosis in like 2013 or 2014.
So if you’re looking to lose weight, I’d recommend going off gluten, whether or not you have evidence of a sensitivity, because it’s just present in so many processed foods that are so addictive. Or if you want to check whether gluten sensitivity is actually a factor in your weight loss resistance, you can try a short-term elimination for 4 weeks. Without changing anything else, track on a weekly basis your weight, waist measurement at the belly button and any other symptoms from gastrointestinal to skin to headaches, brain fog, etc. and check if you feel better off gluten. If you want to make it super objective, try to replace gluten-based foods with equivalent gluten-free foods, although I wouldn’t recommend breads and desserts and regular pastas for someone trying to lose weight. Be sure to closely check your food, medication, and supplement labels for hidden gluten. Then you can try reintroducing gluten by eating a couple normal sized servings in a day and evaluate your response over the next 3 days.
Finally, I’ll finish up with the more obvious interventions for weight loss but with an eye toward developing and maintaining healthy gut microbiota. You’ll want to incorporate plenty of polyphenols into your diet, which are micronutrients recognized for their antioxidant properties, disease prevention and positive effects on the balance of beneficial gut bacteria. They are found in colorful fruits and vegetables, or products like Poly-Prebiotic powder by Pure Encapsulations*. Great food sources of polyphenols include cocoa powder, berries, dried herbs and spices, hazelnuts, chestnuts, pecans, and red, purple, orange, yellow and dark-green vegetables, as well as beverages like green and black tea. Embracing these polyphenol-rich foods can contribute to a healthier gut microbiome and support weight loss.
Fiber, along with polyphenols, is also recognized as a functional food that provides food for the fermentation of beneficial bacteria in the gut, leading to increased short chain fatty acids like butyrate. Found in undigestible carbohydrates from fruits, vegetables, beans, legumes and nuts, fiber serves as an excellent nourishment source for beneficial bacteria. Gut health is extremely influenced by fiber, evident in the distinctive gut microbiota of individuals consuming animal-based diets versus those favoring plant-based diets. High intake of meat, eggs, and cheeses with low fiber content results in an abnormal gut microbiome characterized by reduced fermentation. Additionally, individuals consuming substantial amounts of animal fat face an elevated risk of pathogenic bacteria, potentially linked to increased iron consumption. In contrast, those with higher intake of plant-based prebiotic fiber from fruits and vegetables exhibit an abundance of healthy bacteria in their guts. Note, however, that this does not apply to ketogenic diets, which bypass the traditional production of butyrate through fiber fermentation and instead produce ketone bodies like acetoacetate and beta-hydroxybutyrate and isobutyrate, a metabolite of protein fermentation, which also help with keeping the lining of the colon hypoxic.
That being said, I am generally a supporter of an unprocessed, omnivorous diet with adequate protein, which is basically one gram per pound of ideal body weight a day, including mostly lean animal proteins, at least 2 servings of fatty fish a week, limited saturated fats but from high quality pastured-raised sources like meat, butter or ghee from organic, pasture-raised animals. Dairy is okay if you have no sensitivity, again from pasture-raised animals, with priority going to fermented dairy like yogurt and kefir and hard cheeses in limited quantities. Then healthy fats from nuts, seeds, avocados and healthy oils like extra virgin olive, avocado, Zero Acre Oil*, which is a fermented oil high in Omega 3’s that tolerates high heat cooking, or flaxseeds or flaxseed oil or walnuts in particular for Omega 3’s if you’re not otherwise supplementing with Omega 3’s or getting them from fish. And then getting a rainbow of fruits and veggies with a minimum of 5 servings a day and preferably as many as 9 servings a day. And then for starches, the best choices are starchy vegetables other than white potatoes, so root veggies, winter squash, sweet potatoes, yams and legumes, quinoa and other whole grains, brown rice, black rice, wild rice or cooked, cooled and either eaten cold or only slightly reheated white potatoes and white rice, which are good sources of resistant starch, which functions like fiber in the body and in particular feeds those butyrate producers.
Generally, to lose weight, most women need to stick to no more than 2, ½ cup servings of these types of starchy foods a day and men may be able to get away with a little more. And if your diet is very far from this, I’d suggest picking one area to tackle each week to move more towards a diet like this so that the changes won’t be overwhelming and will be sustainable.
If you’re looking for help with weight loss, I still work with clients in this area both from the food, mental and lifestyle perspectives through a weekly program that runs for 12 weeks, as well as incorporating testing and interpretation to see what’s going on metabolically that might be impeding weight loss. Or if you are struggling with bloating, gas, burping, nausea, constipation, diarrhea, soft stool, acid reflux, IBS, IBD, SIBO, candida overgrowth, fatigue or migraines and want to get to the bottom of it, that’s what I help my clients with. 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 3- and 5- appointment health coaching programs 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.
