The Wahls lab has published a new paper(1) detailing the results of a study that compared how the low saturated fat (Swank) diet and modified Paleolithic (Wahls) diet affected the gut microbiome. In this blog, I’ll talk about what we found, what it means for you, and how you can use this information to optimize your own microbiome.
In this paper, we analyzed the data that was collected as part of a sub-study comparing the Swank diet with the Wahls diet.(2) As part of this study, we were able to collect stool specimens from people during the initial observation period, and at 12 and 24 weeks. Participants in the study were randomly selected for one of the two diets, and machine learning (AI) was used to analyze their microbiome during both phases of the study.
Then, we asked if the microbiome data collected during the observation period could predict whether a person’s fatigue severity would be more significantly reduced. And the answer was yes!
Baseline bacteria in the stool did predict whether the person was more likely to see their fatigue severity significantly reduced. What is particularly interesting is that one set of bacteria predicted a good response to the low saturated fat diet, while a different set of bacteria predicted a good response to the modified Paleolithic diet.
Why would that be the case?
Here is our thinking: The food we eat is first digested by our stomach acid, followed by our digestive enzymes.
After that, the bacteria that live in our bowels continue to digest and metabolize the parts of our food that we can’t digest and absorb. Bacterial metabolites get absorbed into our bloodstream and interact with our immune system, which also interacts with our brain cells and energy levels.
Depending on which bacteria that are present in the bowels you will make different metabolites in response to food coming down the gut. It is the interaction between the genes we have, the bacteria in our gut and the foods we eat that determine how the foods we eat will impact our health.
We instructed the low saturated fat participants to eat whole grains and more non-starchy vegetables; the modified Paleolithic participants were told to eat meat and 6-9 servings of non-starchy vegetables per day, while avoiding grain, dairy and legumes. Both groups ate more vegetables and consumed less added sugar. It is interesting that different bacteria predicted a better response to low fat diet and better response to the modified Paleolithic diet.
Whether we develop multiple sclerosis (MS) or other autoimmune diseases is a three-step process. First you must have the genes that increase the risk (there about 300 genes that have been shown to increase the risk ever so slightly for autoimmune diagnosis).(3) The second step is some sort of infection (there are 20+ bacteria and viruses that increase the risk; but most people have gotten one or more of these infections without getting multiple sclerosis).(4) And third, is the environmental factors that include diet, exercise, toxin exposures, early life stress, obesity, vitamin D and more.(3) Notably, increased exposure to antibiotics, which have a significant impact on the microbiome, also increase the risk of developing MS and autoimmunity.(5)
While you can’t change your genes, infections, or prior use of antibiotics, you can change your diet and other lifestyle factors. First, reduce added sugar and white flour-based foods. Ultra-processed foods increase the risk of developing autoimmune diseases, obesity, diabetes, and mental health problems.(6) Next, add more non-starchy vegetables and sufficient protein, whether it’s animal protein or legumes combined with grain to make a complete protein.
If you have taken antibiotics early in life or multiple rounds of antibiotics as an adult, you are more likely to have a yeast overgrowth in your gut that increases the risk of autoimmunity and mental health issues. In that case, reducing how many carbohydrates you eat would be helpful. An herbal supplement, like Candida Clear, suppresses the yeast without harming the beneficial bacteria. Our gut microbiome is set by the time we are 2 ½ years old and our microbiome will revert back to what we had as a 2 ½ year old after we have a case of vomiting or diarrhea. People who had antibiotics in the first two years of life or multiple rounds of antibiotics as an adult are more likely to have deveoped an overgrowth of yeast in the gut.
That overgrowth of yeast is linked to higher rates of anxiety, depression and autoimmune symptoms. As a result, many who had early antibiotics or prolonged or multiple rounds of antibiotics as adults feel better if they adopt a lower carbohydrate diet and take a herbal product to suppress yeast. They also often feel better when they take probiotics to get more of the health supportive bacteria, like Probiotic MD, and eat more probiotic foods like sauerkraut, kimchi, yoghurt and kefirs. For my dairy-free patients, I recommend nut and coconut milk yoghurts and kefirs.
There will be a time that people will be able to see their medical team, give a sample of saliva, urine, blood, and stool, and receive a detailed, accurate analysis of their genetics, microbiome, and biomarkers, along with recommendations for which dietary approaches would be most helpful.
In the meantime, ask your parents about your early antibiotic exposure. Ask yourself about your lifetime and recent antibiotic exposure. And then adjust your diet and consider adding Candida Clear and Probiotic MD to optimize your microbiome.
Citations
- Meza LA, Fitzjerrells RL, Shemirani F, Titcomb TJ, Rubenstein LM, Eyck PT, et al. Predicting Dietary Impact on Multiple Sclerosis-Related Symptoms With the Gut Microbiome: A Pilot Study Using Unsupervised Machine Learning. Brain Behav. 2026;16(4):e71394.
- Wahls TL, Titcomb TJ, Bisht B, Eyck PT, Rubenstein LM, Carr LJ, et al. Impact of the Swank and Wahls elimination dietary interventions on fatigue and quality of life in relapsing-remitting multiple sclerosis: The WAVES randomized parallel-arm clinical trial. Mult Scler J Exp Transl Clin. 2021;7(3):20552173211035399.
- Leon AM, Lincoln MR. Integrating Genetics and Environment to Find Causal Mechanisms for Multiple Sclerosis. Eur J Immunol. 2026;56(5):e70206.
- Landry RL, Embers ME. The Probable Infectious Origin of Multiple Sclerosis. NeuroSci. 2023;4(3):211-34.
- Salamatullah HK, AboAljadiel L, Halabi MH, Alqurashi S, Aljohani R, Aljafari D, et al. The association between antimicrobial exposure and subsequent multiple sclerosis risk: A systematic review and meta-analysis. Mult Scler Relat Disord. 2026;107:106936.
- Lane MM, Gamage E, Du S, Ashtree DN, McGuinness AJ, Gauci S, et al. Ultra-processed food exposure and adverse health outcomes: umbrella review of epidemiological meta-analyses. BMJ. 2024;384:e077310.
