From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality.
From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality.
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从微生物学基因到生态系统：建模方法和个性的重要性
DOI：
10.3389/fmicb.2017.02299
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发表时间：
2017
影响因子：
5.2
通讯作者：
Hellweger FL
中科院分区：
文献类型：
--
作者：
Kreft JU;Plugge CM;Prats C;Leveau JHJ;Zhang W;Hellweger FL
模型是研究微生物生态学的重要工具。它们可以用来通过帮助解释观察和检验假设来促进理解，并预测生态系统管理行动或不同气候的影响。在过去的几十年里，生物学知识和生态系统观察已经发展到分子水平，特别是基因水平。然而，微生物生态学模型的变化不大，目前的挑战是如何利用遗传水平的知识和观察结果。我们回顾了明确考虑基因并在种群或生态系统水平上做出预测的已发表模型。这些模型可分为三种一般方法，即代谢通量、以基因为中心和基于agent的方法。我们通过将这些方法应用于一个假设的生态系统来描述和对比这些方法，并讨论它们的优缺点。一个重要的区别特征是如何处理单个细胞之间的差异（个性）。在微生物生态系统中，个体异质性是由多种机制产生的，包括分子的随机相互作用（如基因表达）、随机和确定性细胞分裂不对称、小尺度环境异质性和异质性环境中的差异运输。这种异质性可以通过多种机制被放大并转移到其他细胞特性中，包括营养摄取、代谢和生长、细胞周期不同步以及年龄和损伤的影响。例如，随机基因表达可能导致营养摄取酶水平的异质性，从而导致细胞内营养水平的异质性。个性可以产生重要的生态后果，包括劳动分工、下注对冲、老龄化和次优性。了解个体化的重要性及其对特定微生物系统和所调查问题的潜在机制对于选择最佳建模策略至关重要。
Models are important tools in microbial ecology. They can be used to advance understanding by helping to interpret observations and test hypotheses, and to predict the effects of ecosystem management actions or a different climate. Over the past decades, biological knowledge and ecosystem observations have advanced to the molecular and in particular gene level. However, microbial ecology models have changed less and a current challenge is to make them utilize the knowledge and observations at the genetic level. We review published models that explicitly consider genes and make predictions at the population or ecosystem level. The models can be grouped into three general approaches, i.e., metabolic flux, gene-centric and agent-based. We describe and contrast these approaches by applying them to a hypothetical ecosystem and discuss their strengths and weaknesses. An important distinguishing feature is how variation between individual cells (individuality) is handled. In microbial ecosystems, individual heterogeneity is generated by a number of mechanisms including stochastic interactions of molecules (e.g., gene expression), stochastic and deterministic cell division asymmetry, small-scale environmental heterogeneity, and differential transport in a heterogeneous environment. This heterogeneity can then be amplified and transferred to other cell properties by several mechanisms, including nutrient uptake, metabolism and growth, cell cycle asynchronicity and the effects of age and damage. For example, stochastic gene expression may lead to heterogeneity in nutrient uptake enzyme levels, which in turn results in heterogeneity in intracellular nutrient levels. Individuality can have important ecological consequences, including division of labor, bet hedging, aging and sub-optimality. Understanding the importance of individuality and the mechanism(s) underlying it for the specific microbial system and question investigated is essential for selecting the optimal modeling strategy.
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DOI：
10.1073/pnas.0400962101
发表时间：
2004-04-27
影响因子：
11.1
作者：
Castellanos, M;Wilson, DB;Shuler, ML
通讯作者：
Shuler, ML
影响因子：
1.8
作者：
Bucci, Vanni;Nunez-Milland, Daliangelis;Hellweger, Ferdi L.
通讯作者：
Hellweger, Ferdi L.
DOI：
10.1073/pnas.1215340110
发表时间：
2013-01-02
影响因子：
11.1
作者：
Anantharaman, Karthik;Breier, John A.;Dick, Gregory J.
通讯作者：
Dick, Gregory J.
DOI：
10.1126/science.1188658
发表时间：
2010-06-04
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Christen M;Kulasekara HD;Christen B;Kulasekara BR;Hoffman LR;Miller SI
通讯作者：
Miller SI
影响因子：
4.4
作者：
Cottrell, Matthew T.;Kirchman, David L.
通讯作者：
Kirchman, David L.