In June 2017, a small but controlled clinical trial published in the European Journal of Clinical Nutrition compared the gut microbiota of individuals who had followed a Paleo-style diet for at least one year with those on a standard Western diet. The researchers expected to see a clear microbial signature of the Paleo group — higher diversity, more fiber-degrading species, and strong short-chain fatty acid (SCFA) production. What they found was more nuanced, and it offers a valuable lesson for anyone managing elimination diets or dealing with digestive discomfort.
The Study at a Glance
Twenty-four adults participated: 12 long-term Paleo adherents (average 1.5 years on the diet) and 12 matched controls eating a typical Western diet. Stool samples were analyzed for bacterial composition via 16S rRNA sequencing, and SCFA levels were measured. The Paleo group showed significantly higher alpha diversity — a marker often associated with better gut health. However, levels of butyrate, a key SCFA that feeds colon cells and reduces inflammation, were not significantly different between the groups. In fact, some Paleo participants had lower concentrations of butyrate than expected, despite consuming more fiber from vegetables and fruit.
Why Butyrate Might Lag on a Paleo Diet
The study authors proposed that the Paleo diet’s exclusion of grains, legumes, and dairy — all traditional sources of resistant starch and fermentable fibers — might limit the substrates that butyrate-producing bacteria (like Faecalibacterium prausnitzii and Roseburia) need to thrive. While Paleo eaters often get ample soluble fiber from tubers, fruits, and vegetables, the specific types of resistant starch found in cooled potatoes or green bananas may not be sufficient to maintain high butyrate levels for everyone. Additionally, the lower carbohydrate intake typical of some Paleo approaches could reduce overall fermentation in the colon.
This does not mean the Paleo diet is harmful — far from it. The participants reported good digestive comfort and no overt symptoms. But the finding highlights that microbial adaptation to a new dietary pattern is not instantaneous. For someone transitioning from a standard diet to a strict elimination protocol, the gut ecosystem undergoes a restructuring that can take months or even years.
Practical Takeaways for Elimination Dieters
If you are following an autoimmune protocol (AIP) or a strict Paleo elimination phase and still experience occasional bloating or irregular bowels, the 2017 study offers several actionable insights:
- Rotate your vegetable sources. Relying on the same few low-FODMAP vegetables (zucchini, carrots, spinach) can starve certain bacterial populations. Include a variety of tubers, leafy greens, and cruciferous vegetables — even if you need to reintroduce them slowly to assess tolerance.
- Consider cooked and cooled starches. White potatoes, sweet potatoes, and plantains, when cooked and then cooled, form resistant starch that feeds butyrate producers. If you tolerate them, incorporate them a few times per week.
- Patience with reintroductions. The microbiota does not shift overnight. As we saw in the 2016 survey of 1,167 AIP practitioners, many found that reintroduction phases were more challenging than elimination — a finding that aligns with the idea that microbial adaptation is not instant. What the 2016 Survey of 1,167 AIP Practitioners Revealed About Elimination Diets noted that the order and timing of reintroductions mattered greatly for symptom management.
- Monitor more than just food. Sleep, stress, and meal timing influence the microbiome. The Paleo group in the study had lower overall stress markers, which may have contributed to their higher diversity. Prioritize consistency in your daily routine.
Limitations and Individual Variation
The 2017 study was small and cross-sectional, meaning it can show correlation but not causation. It also did not control for the exact composition of each participant’s Paleo diet — some may have included dairy or legumes occasionally, while others were very strict. Moreover, individual genetics and baseline microbiota composition play a huge role in how someone responds to a high-vegetable, grain-free diet. A person with sulfur sensitivity, for example, might react to the high-sulfur content of cruciferous vegetables even if those vegetables are otherwise beneficial for microbial diversity. (We covered practical strategies for that scenario in an earlier post: Overcoming Sulfur Sensitivity on a Paleo Diet: A Practical Guide.)
What This Means for Digestive Comfort
If you have been on a Paleo or AIP elimination diet for several weeks and still notice bloating or gas, it may not be a sign that the diet is wrong for you. Instead, it could reflect the transitional phase of microbial remodeling. The key is to distinguish between a true food intolerance and a normal adaptation signal. A persistent, sharp pain or dramatic change in stool consistency should always be discussed with a healthcare provider. But mild, intermittent bloating that lessens over time is often a sign that your gut is repopulating with new species.
For those currently in an elimination phase, consider keeping a log not just of foods but also of stool consistency and timing of meals relative to symptoms. This data, when shared with a practitioner, can help distinguish between normal adaptation and a true intolerance. It also allows you to see patterns — for instance, whether bloating occurs more after meals that include high-FODMAP vegetables (like onions or garlic) or after larger portions of resistant starch. Over the course of several months, you may notice that your tolerance expands as your microbiota adjusts.
