Los Alamos National Laboratory, Los Alamos, NM, USA.
University of Neuchâtel, Neuchâtel, Switzerland.
Microbiome. 2023 Aug 26;11(1):192. doi: 10.1186/s40168-023-01634-7.
As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.
随着微生物组研究的进展，越来越明显的是，大多数（如果不是全部）真核生物都是由原核生物、其他真核生物和病毒组成的微生物组的宿主。最近才将真菌视为具有自己微生物组的整体共生体，因为已经发现丝状真菌在其菌丝内含有细菌（包括蓝细菌）、真菌病毒、其他真菌和整个藻类细胞。使用多组学方法研究了这种复杂的内生微生物组的组成部分。然而，由于缺乏用于小型微生物组（例如，细胞内微生物组）的综合多组学的工具、技术和标准化，限制了对内生微生物组的总多样性及其对真菌宿主的功能影响的研究和理解。了解微生物组对真菌宿主的影响将推进对“微生物组内的微生物组”如何影响更广泛的微生物群落动态和生态功能的探索。本文讨论了在内生微生物组上进行综合多组学研究的最新进展和正在面临的挑战。解决与样品提取、样品制备、多组学数据生成以及多组学数据分析和整合相关的挑战将有助于推进对内生微生物组的现有认识，并为将微生物组研究缩小到更小的规模提供路线图。视频摘要。
