多组学在水工程微生物生态学中的应用前景
Prospects for Multi-omics in the Microbial Ecology of Water Engineering
摘要：
近三十年来，高通量测序技术和生物信息学方法的进步大大提高了我们探索微生物及其功能的能力，包括那些尚未完全分离培养的微生物。基因组解析宏基因组学方法已经能够将强大的功能预测与特定的分类组联系起来，并具有越来越高的保真度。此外，全群落基因表达调查和代谢物分析使得能够直接调查特定环境中的群落规模功能。这些进展使微生物组科学从描述性研究转向机械和预测性框架，以设计和利用微生物群落来实现所需的有益结果。在这里，我们回顾了现代基因组解析宏基因组方法已被应用于各种水工程应用，从实验室规模的生物反应器，以全面的系统。我们描述了跨工程水系统的综合组学分析以及将这些见解与建模方法配对的基础。最后，我们总结了新兴的omics为基础的技术，我们相信将是强大的工具，水工程应用。总的来说，我们为专门从事水工程的微生物生态学家提供了一个框架，将尖端的组学方法应用于他们的研究问题，以实现新的功能见解。在工程水系统中成功采用预测框架可以随着对水和能源资源的需求增加而实现更具经济和环境可持续性的生物过程。
英文摘要：
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions-including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, whole community gene expression surveys and metabolite profiling have permitted direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.
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