Contribution of genome-scale metabolic modelling to niche theory,Ecology Letters

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Contribution of genome-scale metabolic modelling to niche theory
Ecology Letters ( IF 7.6 ) Pub Date : 2022-04-05 , DOI: 10.1111/ele.13954
Antoine Régimbeau ₁ , Marko Budinich ₁ , Abdelhalim Larhlimi ₁ , Juan José Pierella Karlusich ₂ , Olivier Aumont ₃ , Laurent Memery ₄ , Chris Bowler _{2,

5} , Damien Eveillard _{1,

5}

Affiliation

Standard niche modelling is based on probabilistic inference from organismal occurrence data but does not benefit yet from genome-scale descriptions of these organisms. This study overcomes this shortcoming by proposing a new conceptual niche that resumes the whole metabolic capabilities of an organism. The so-called metabolic niche resumes well-known traits such as nutrient needs and their dependencies for survival. Despite the computational challenge, its implementation allows the detection of traits and the formal comparison of niches of different organisms, emphasising that the presence–absence of functional genes is not enough to approximate the phenotype. Further statistical exploration of an organism's niche sheds light on genes essential for the metabolic niche and their role in understanding various biological experiments, such as transcriptomics, paving the way for incorporating better genome-scale description in ecological studies.

中文翻译：

基因组规模代谢模型对生态位理论的贡献

标准生态位建模基于生物体发生数据的概率推断，但尚未受益于这些生物体的基因组规模描述。这项研究通过提出一个新的概念生态位来克服这一缺点，该生态位可以恢复生物体的全部代谢能力。所谓的代谢生态位恢复了众所周知的特征，例如营养需求及其生存依赖性。尽管存在计算挑战，但它的实施允许检测特征和对不同生物的生态位进行正式比较，强调功能基因的存在-不存在不足以近似表型。对生物生态位的进一步统计探索揭示了代谢生态位所必需的基因及其在理解各种生物实验中的作用，

更新日期：2022-04-05

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