Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.
Microbiome. 2024 Sep 28;12(1):184. doi: 10.1186/s40168-024-01868-z.
The potential promise of the microbiome to ameliorate a wide range of societal and ecological challenges, from disease prevention and treatment to the restoration of entire ecosystems, hinges not only on microbiome engineering but also on the stability of beneficial microbiomes. Yet the properties of microbiome stability remain elusive and challenging to discern due to the complexity of interactions and often intractable diversity within these communities of bacteria, archaea, fungi, and other microeukaryotes. Networks are powerful tools for the study of complex microbiomes, with the potential to elucidate structural patterns of stable communities and generate testable hypotheses for experimental validation. However, the implementation of these analyses introduces a cascade of dichotomies and decision trees due to the lack of consensus on best practices. Here, we provide a road map for network-based microbiome studies with an emphasis on discerning properties of stability. We identify important considerations for data preparation, network construction, and interpretation of network properties. We also highlight remaining limitations and outstanding needs for this field. This review also serves to clarify the varying schools of thought on the application of network theory for microbiome studies and to identify practices that enhance the reproducibility and validity of future work. Video Abstract.
微生物组具有改善广泛的社会和生态挑战的潜力，从疾病预防和治疗到整个生态系统的恢复，不仅取决于微生物组工程，还取决于有益微生物组的稳定性。然而，由于这些细菌、古菌、真菌和其他微型真核生物群落中相互作用的复杂性以及通常难以处理的多样性，微生物组稳定性的性质仍然难以捉摸，难以辨别。网络是研究复杂微生物组的有力工具，具有阐明稳定群落结构模式的潜力，并为实验验证生成可测试的假设。然而，由于缺乏关于最佳实践的共识，这些分析的实施引入了一系列二分法和决策树。在这里，我们提供了一个基于网络的微生物组研究路线图，重点是辨别稳定性的属性。我们确定了数据准备、网络构建和网络属性解释的重要考虑因素。我们还强调了该领域仍然存在的局限性和未满足的需求。本综述还旨在澄清应用网络理论进行微生物组研究的不同学派的观点，并确定增强未来工作的可重复性和有效性的实践。视频摘要。
