Ecosystem-specific microbiota and microbiome databases in the era of big data.
Ecosystem-specific microbiota and microbiome databases in the era of big data.
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DOI：
10.1186/s40793-022-00433-1
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发表时间：
2022-07-16
影响因子：
7.9
通讯作者：
中科院分区：
文献类型：
--
作者：
在过去的几十年中，测序方法的快速发展加速了微生物群和微生物组研究的潜在范围和深度。该领域的最新发展的特点是从纯粹的分类研究扩展到对社区功能的更大调查。由于深入的基因组和环境覆盖范围通常在主要分类群和生态系统中分布不均匀，因此可能很难识别或证实微生物群落内的关系。包含来自不同生态系统的数据集的通用数据库开辟了一个数据可访问性的新时代，尽管在数据质量和异质性方面存在成本。这一挑战很容易体现在元组学数据与特定生境标准的整合中，这些标准有助于在样本处理和生态系统背景方面对数据集进行情境化。大型基因组库的一个特殊情况，生态系统特定数据库（ES-DB），已经出现，以巩固和更好地简化样本处理和分析协议，围绕个别生态系统的研究，使独立的研究，以产生可比的数据集。在这里，我们提供了一个全面的审查这一新兴的工具，微生物群落分析在该领域的当前趋势。我们专注于导致ES-DB的形成的因素，它们与传统微生物数据库的比较，ES-DB与元组学平台集成的潜力，以及ES-DB的适用性的固有限制。
The rapid development of sequencing methods over the past decades has accelerated both the potential scope and depth of microbiota and microbiome studies. Recent developments in the field have been marked by an expansion away from purely categorical studies towards a greater investigation of community functionality. As in-depth genomic and environmental coverage is often distributed unequally across major taxa and ecosystems, it can be difficult to identify or substantiate relationships within microbial communities. Generic databases containing datasets from diverse ecosystems have opened a new era of data accessibility despite costs in terms of data quality and heterogeneity. This challenge is readily embodied in the integration of meta-omics data alongside habitat-specific standards which help contextualise datasets both in terms of sample processing and background within the ecosystem. A special case of large genomic repositories, ecosystem-specific databases (ES-DB’s), have emerged to consolidate and better standardise sample processing and analysis protocols around individual ecosystems under study, allowing independent studies to produce comparable datasets. Here, we provide a comprehensive review of this emerging tool for microbial community analysis in relation to current trends in the field. We focus on the factors leading to the formation of ES-DB’s, their comparison to traditional microbial databases, the potential for ES-DB integration with meta-omics platforms, as well as inherent limitations in the applicability of ES-DB’s.
世界病毒学学会首次国际会议：应对全球病毒流行。
影响因子：
3.7
作者：
Söderlund-Venermo M;Varma A;Guo D;Gladue DP;Poole E;Pujol FH;Pappu H;Romalde JL;Kramer L;Baz M;Venter M;Moore MD;Nevels MM;Ezzikouri S;Vakharia VN;Wilson WC;Malik YS;Shi Z;Abdel-Moneim AS
通讯作者：
Abdel-Moneim AS