Genome-level Constraint-Based Analysis of Megasphaera sp. MJR8396C Reveals Dual Metabolic Roles in the Human Gut

Understanding the metabolic behavior of gut bacteria is crucial for developing targeted microbiome-based interventions in obesity. In this study, we investigated the metabolic flexibility of Megasphaera sp. MJR8396C , an understudied gut microbe implicated in altered microbiota functionality, using constraint-based reconstruction and analysis (COBRA). Our findings demonstrate that COBRA, combined with flux balance analysis (FBA), offers a comprehensive framework to elucidate microbial metabolism under diverse nutritional environments. We reveal that the metabolic outputs of Megasphaera sp. MJR8396C significantly vary depending on nutrient availability, genetic interventions, and microbial community context. Specifically, Megasphaera sp. MJR8396C can engage in Stickland-type amino acid fermentation and produce both beneficial metabolites such as butyrate, and potentially harmful by-products like ammonia. The ambiguous role of this bacterium—being beneficial or detrimental in obesity—is context-dependent, emphasizing the importance of metabolic environment modulation. We further show that computational tools such as OptForce and co-culture modeling can guide real-time interventions, including genetic modifications or community adjustments, to optimize bacterial metabolic profiles. These results highlight the potential of systems biology approaches to address knowledge gaps and strategically harness gut microbes for therapeutic outcomes.