If you’re on keto or just looking for a sugar swap that truly works, D-allulose could be the game-changer you didn’t know you needed. This rare, low-calorie sugar has been gaining momentum as a sweetener, but the key question is: does it mess with your gut bacteria or cause digestive troubles like so many others?
A major study from 2025 offers some reassuring (and surprising) news. While popular sugar alcohols like xylitol, erythritol, and sorbitol are notorious for causing gas and bloating, and some artificial sweeteners can even disrupt gut microbiome balance and spike your blood sugar response, D-allulose seems to behave differently.
Scientists focused on whether gut bacteria can even metabolize this sweetener. They looked for a special enzyme—D-allulose-6-phosphate 3-epimerase (AlsE)—needed for bacteria to use allulose as food. Out of over 85,000 bacterial genomes checked, only 116 species had this gene, and just 35 of those commonly live in the human gut. In real-world samples from healthy adults, only 15.8% had detectable alsE in their gut bacteria, and actual gene expression was rare. Lab experiments found that, of common gut bugs, only Clostridium innocuum could consistently utilize D-allulose as a carbon source.
What does this mean for you? D-allulose is barely fermented by your gut microbes, leading to less gas, little to no diarrhea, and few (if any) changes in your microbiota. Plus, clinical studies suggest you can enjoy it even at higher doses without tummy trouble.
Bottom line: If you’re on keto or cutting sugar for health reasons, D-allulose looks like a safe bet—sweet but gentle on your gut, with minimal interference to your microbiome. And for the small percentage of people whose gut microbes can handle allulose? So far, there’s no solid evidence that it’s a problem.
Source: Nutrients
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