Dietary fiber fermentation restores microbiome resilience to oxygen stress in a host-independent ex vivo model

ABSTRACT Gut dysbiosis is often driven by the loss of beneficial obligate anaerobes and the overgrowth of pathobiont facultative anaerobes, a shift perpetuated by oxygen buildup in the gut lumen. We hypothesized that dietary fibers could restore microbiome resilience to oxygen disruption by fueling short-chain fatty acid (SCFA) production and acidifying the environment to inhibit the blooming of pathobiont facultative anaerobes. To test this hypothesis independent of the host, fecal samples from healthy donors were cultured ex vivo under four conditions: Control, Oxygen-only (5%), Fiber-only, and Oxygen+Fiber. Guild-level analysis of 16S rRNA gene V4 region sequencing revealed that oxygen alone drove a significant expansion of co-abundant groups (CAGs; CAG2, CAG3) with facultative anaerobes, specifically amplicon sequence variants (ASVs) from Enterobacteriaceae. However, fiber supplementation under microaerophilic conditions fueled robust SCFA production and lowered pH, which effectively suppressed these oxygen-promoted pathobionts. Crucially, fiber restored the abundance of guilds (CAG15, CAG17) with key SCFA-producing obligate anaerobes, such as Eubacterium and Roseburia , which were otherwise inhibited by oxygen. Furthermore, we identified a unique guild (CAG19) containing Bifidobacterium that thrived specifically in the oxygen-fiber environment, suggesting a transitional role in restoring homeostasis. These findings demonstrate that dietary fibers can directly restore microbiome resilience against oxygen stress, offering a mechanistic strategy for managing dysbiosis-related conditions. IMPORTANCE This study demonstrates that dietary fibers can protect short-chain fatty acid (SCFA)-producing obligate anaerobes under microaerophilic conditions in a host-independent manner. Unlike antioxidants that scavenge oxygen, fibers provide fermentable substrates that fuel microbial metabolism, lowering pH and creating a chemical environment that suppresses oxygen-tolerant pathobionts. Using an ex vivo fermentation model, we show that fiber drives the emergence of a Bifidobacterium -centered “transitional guild” that promotes the recovery of strict anaerobes, highlighting a microbe-fueled resilience mechanism. These findings reveal how dietary fibers directly stabilize the microbial community and support targeted high-fiber interventions to prevent dysbiosis.