An important goal for many nutrition-based microbiome studies is to identify the metabolic function of microbes in complex microbial communities and its impact on host physiology. This research can be confounded by poorly-understood effects of community composition and host diet on the metabolic traits of individual taxa. Here, we investigated these multi-way interactions by constructing and analyzing metabolic models comprising every combination of five bacterial members of the Drosophila gut microbiome (from single taxa to the five-member community of Acetobacter and Lactobacillus species) under three nutrient regimes. We show that the metabolic function of Drosophila gut bacteria is dynamic, influenced by community composition and responsive to dietary modulation. Furthermore, we show that ecological interactions such as competition and mutualism identified from the growth patterns of gut bacteria are underlain by a diversity of metabolic interactions, and show that the bacteria tend to compete for amino acids and B vitamins more frequently than for carbon sources. Our results reveal that in addition to fermentation products such as acetate, intermediates of the tricarboxylic acid (TCA) cycle including 2-oxoglutarate and succinate are produced at high flux and cross-fed between bacterial taxa suggesting important roles for TCA cycle intermediates in modulating Drosophila gut microbe interactions and the potential to influence host traits. These metabolic models provide specific predictions of the patterns of ecological and metabolic interactions among gut bacteria under different nutrient regimes, with potentially important consequences for overall community metabolic function and nutritional interactions with the host.

中文翻译：

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果蝇肠道菌群的预测代谢功能

许多基于营养的微生物组研究的重要目标是确定复杂微生物群落中微生物的代谢功能及其对宿主生理的影响。社区组成和寄主饮食对单个类群代谢特征的影响认识不足，可能会混淆这项研究。在这里，我们通过构建和分析代谢模型来研究这些多途径的相互作用，该代谢模型包括果蝇肠道微生物组中五个细菌成员（从单个分类群到醋杆菌和乳酸杆菌物种的五个成员群落）的五个细菌成员的每种组合，并在三种营养体系下进行。我们显示，果蝇肠道细菌的代谢功能是动态的，受社区组成的影响，并对饮食的调制有反应。此外，我们表明，从肠道细菌的生长方式中识别出的竞争性和共生性等生态相互作用是各种代谢相互作用的基础，并且表明细菌比氨基酸更倾向于竞争氨基酸和B族维生素。我们的结果表明，除了发酵产物（如乙酸盐）外，包括2-氧戊二酸和琥珀酸酯在内的三羧酸（TCA）循环中间体也以高通量产生，并且在细菌类群之间交叉进食，这表明TCA循环中间体在调节果蝇中具有重要作用。肠道微生物相互作用和影响宿主性状的潜力。这些新陈代谢模型提供了在不同养分制度下肠道细菌之间生态和代谢相互作用模式的具体预测，