Department of Environmental Systems Science, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland.
Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland.
Nat Microbiol. 2024 Dec;9(12):3097-3109. doi: 10.1038/s41564-024-01850-3. Epub 2024 Nov 26.
Microbiome metabolism underlies numerous vital ecosystem functions. Individual microbiome members often perform partial catabolism of substrates or do not express all of the metabolic functions required for growth. Microbiome members can complement each other by exchanging metabolic intermediates and cellular building blocks to achieve a collective metabolism. We currently lack a mechanistic framework to explain why microbiome members adopt partial metabolism and how metabolic functions are distributed among them. Here we argue that natural selection for proteome efficiency-that is, performing essential metabolic fluxes at a minimal protein investment-explains partial metabolism of microbiome members, which underpins the collective metabolism of microbiomes. Using the carbon cycle as an example, we discuss motifs of collective metabolism, the conditions under which these motifs increase the proteome efficiency of individuals and the metabolic interactions they result in. In summary, we propose a mechanistic framework for how collective metabolic functions emerge from selection on individuals.
微生物组代谢是许多重要生态系统功能的基础。单个微生物组成员通常只能部分分解基质，或者无法表达生长所需的所有代谢功能。微生物组成员可以通过交换代谢中间产物和细胞构建块来互补，从而实现集体代谢。目前，我们缺乏一个解释微生物组成员为什么采用部分代谢以及代谢功能如何在它们之间分配的机制框架。在这里，我们认为，为了提高蛋白质组效率而进行的选择——即在最小的蛋白质投入下进行必要的代谢通量——解释了微生物组成员的部分代谢，这是微生物组集体代谢的基础。我们使用碳循环作为一个例子，讨论了集体代谢的模式，以及这些模式在何种条件下提高个体的蛋白质组效率，并导致它们产生代谢相互作用。总之，我们提出了一个关于集体代谢功能如何从个体选择中产生的机制框架。
