Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Systems Biology Group, Amsterdam Institute for Life and Environment (A-LIFE) and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
Nat Microbiol. 2023 Oct;8(10):1799-1808. doi: 10.1038/s41564-023-01458-z. Epub 2023 Aug 31.
Heterotrophic bacteria-bacteria that utilize organic carbon sources-are taxonomically and functionally diverse across environments. It is challenging to map metabolic interactions and niches within microbial communities due to the large number of metabolites that could serve as potential carbon and energy sources for heterotrophs. Whether their metabolic niches can be understood using general principles, such as a small number of simplified metabolic categories, is unclear. Here we perform high-throughput metabolic profiling of 186 marine heterotrophic bacterial strains cultured in media containing one of 135 carbon substrates to determine growth rates, lag times and yields. We show that, despite high variability at all levels of taxonomy, the catabolic niches of heterotrophic bacteria can be understood in terms of their preference for either glycolytic (sugars) or gluconeogenic (amino and organic acids) carbon sources. This preference is encoded by the total number of genes found in pathways that feed into the two modes of carbon utilization and can be predicted using a simple linear model based on gene counts. This allows for coarse-grained descriptions of microbial communities in terms of prevalent modes of carbon catabolism. The sugar-acid preference is also associated with genomic GC content and thus with the carbon-nitrogen requirements of their encoded proteome. Our work reveals how the evolution of bacterial genomes is structured by fundamental constraints rooted in metabolism.
异养细菌是利用有机碳源的细菌，在不同的环境中具有丰富的分类和功能多样性。由于可能有大量的代谢物可以作为异养生物的潜在碳源和能源，因此很难绘制微生物群落中的代谢相互作用和生态位。它们的代谢生态位是否可以用简化的代谢类别等少数通用原则来理解尚不清楚。在这里，我们对在含有 135 种碳底物之一的培养基中培养的 186 株海洋异养细菌菌株进行了高通量代谢谱分析，以确定生长速率、迟滞时间和产率。我们表明，尽管在所有分类学水平上都存在高度的可变性，但异养细菌的分解代谢生态位可以根据它们对糖酵解（糖）或糖异生（氨基酸和有机酸）碳源的偏好来理解。这种偏好由两种碳利用途径中进入的途径所包含的基因总数编码，并且可以使用基于基因计数的简单线性模型进行预测。这允许根据流行的碳分解代谢模式来描述微生物群落的粗粒度描述。糖 - 酸的偏好也与基因组 GC 含量相关，因此与它们编码的蛋白质组的碳氮需求相关。我们的工作揭示了细菌基因组的进化是如何受到代谢中根深蒂固的基本限制所影响的。
