Sphingopyxis granuli strain TFA is an α-proteobacterium that belongs to the sphingomonads, a group of bacteria well-known for its degradative capabilities and oligotrophic metabolism. Strain TFA is the only bacterium in which the mineralisation of the aromatic pollutant tetralin has been completely characterized at biochemical, genetic, and regulatory levels and the first Sphingopyxis characterised as facultative anaerobe. Here we report additional metabolic features of this α-proteobacterium using metabolic modelling and the functional integration of genomic and transcriptomic data. The genome-scale metabolic model (GEM) of strain TFA, which has been manually curated, includes information on 743 genes, 1114 metabolites and 1397 reactions. This represents the largest metabolic model for a member of the Sphingomonadales order thus far. The predictive potential of this model was validated against experimentally calculated growth rates on different carbon sources and under different growth conditions, including both aerobic and anaerobic metabolisms. Moreover, new carbon and nitrogen sources were predicted and experimentally validated. The constructed metabolic model was used as a platform for the incorporation of transcriptomic data, generating a more robust and accurate model. In silico flux analysis under different metabolic scenarios highlighted the key role of the glyoxylate cycle in the central metabolism of strain TFA.

颗粒鞘氨醇菌株 TFA 是一种 α-变形菌，属于鞘氨醇单胞菌，鞘氨醇单胞菌是一类以其降解能力和寡营养代谢而闻名的细菌。TFA 菌株是唯一一种在生化、遗传和调控水平上完全表征了芳香族污染物四氢化萘矿化的细菌，也是第一个被表征为兼性厌氧菌的鞘氨醇细菌。在这里，我们使用代谢模型以及基因组和转录组数据的功能整合报告了这种 α-变形菌的其他代谢特征。TFA 菌株的基因组规模代谢模型 (GEM) 是手动策划的，包含 743 个基因、1114 个代谢物和 1397 个反应的信息。这代表了迄今为止鞘氨醇目成员最大的代谢模型。该模型的预测潜力通过实验计算的不同碳源和不同生长条件（包括有氧和无氧代谢）下的生长速率进行了验证。此外，还预测并通过实验验证了新的碳源和氮源。构建的代谢模型用作整合转录组数据的平台，生成更稳健和准确的模型。不同代谢场景下的计算机通量分析强调了乙醛酸循环在菌株 TFA 的中心代谢中的关键作用。