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Rare genes in bacterial pangenomes have historically been considered non-essential, dispensable, or even costly, and largely excluded from in-depth analyses due to their perceived redundancy, high variability, and presumed neutral evolutionary origin. However, whether rare genes contribute to metabolic robustness when core genes are lost remains an open question. In this study, we systematically investigate the role of rare metabolic genes in Escherichia coli, revealing their essentiality in maintaining metabolic functions under core gene loss. Through a pangenome-scale reconstruction of 15311 strain-specific genome-scale models (panGEM) and over 22.4 million gene knockout simulations, we demonstrate that: (i) 9.4% of rare metabolic genes are essential in at least one of three key host environments—feces, serum, and urine; (ii) 41% of strains rely on at least one rare essential metabolic gene for survival; (iii) rare metabolic genes emerge as a result of microniche adaptation, and (iv) panGEM allows for the prediction of a subset of highly conserved metabolic reactions with minimal genetic diversity as stable drug targets. These findings challenge the common view that rare genes primarily serve as evolutionary byproducts of genome fluidity and reveal their critical role in metabolic resilience.细菌泛基因组（bacterial pangenomes）中的稀有基因长期以来被视为非必需、可缺失甚至具有进化代价的基因，且由于其被认为存在冗余、变异性高且进化起源大概率为中性，故而在深度分析中大多被排除在外。然而，当核心基因缺失时，稀有基因是否有助于维持代谢稳健性（metabolic robustness）仍是一个悬而未决的问题。 本研究系统探究了大肠杆菌（Escherichia coli）中稀有代谢基因的功能，揭示了其在核心基因缺失状态下维持代谢功能的必要性。通过构建15311株菌株特异性基因组规模模型（panGEM）并开展泛基因组尺度的重构与超过2240万次基因敲除模拟，本研究证实了以下结论：（i）9.4%的稀有代谢基因在粪便、血清与尿液这三种关键宿主环境中的至少一种环境下具有必需性；（ii）41%的菌株需要至少一种稀有必需代谢基因才能存活；（iii）稀有代谢基因的产生源于微生态位适应（microniche adaptation）；（iv）panGEM可用于预测一类遗传多样性极低的高度保守代谢反应作为稳定药物靶点。 这些发现挑战了"稀有基因主要是基因组流动性的进化副产物"这一主流观点，并揭示了其在代谢韧性（metabolic resilience）中的关键作用。