Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan.
Curr Protoc. 2021 May;1(5):e128. doi: 10.1002/cpz1.128.
It is critical to identify individual genomes from microbiomic samples in order to carry out analysis of the microbes. Methods based on existing databases, however, may have limited capabilities in elucidating and quantifying the microbes due to the largely unidentified microbial species in natural or human-associated environments. We thus developed a database-free method, MaxBin 2.0, to aid in the process of recovering microbial genomes from metagenomes in a de novo manner. The recovery of individual genomes allows analysis of the microbiome in terms of a collection of microbial genomes so that one can understand the functional roles of each species. The data of individual microbes may then be analyzed collectively to untangle the interactions between different microbial organisms. By reporting the genome abundance information for co-assembled metagenomes, one may also identify which microorganisms dominate the microbiome and which species may co-occur from the MaxBin 2.0 results. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Recovering genomes from one shotgun metagenome with coverage information Basic Protocol 2: Recovering genomes from one shotgun metagenome without coverage information Basic Protocol 3: Recovering genomes given multiple shotgun metagenomes with coverage information for each metagenome Basic Protocol 4: Recovering genomes given multiple shotgun metagenomes without coverage information Support Protocol 1: MaxBin installation Support Protocol 2: Assembling and co-assembling NGS reads.
为了对微生物进行分析，从微生物组样本中识别个体基因组至关重要。然而，基于现有数据库的方法由于在自然或人类相关环境中存在大量未被识别的微生物物种，因此在阐明和量化微生物方面的能力可能有限。因此，我们开发了一种无数据库的方法 MaxBin 2.0，以帮助从宏基因组中以全新的方式恢复微生物基因组。单个基因组的恢复允许根据微生物基因组的集合来分析微生物组，从而可以理解每个物种的功能角色。然后可以集体分析单个微生物的数据，以理清不同微生物之间的相互作用。通过报告共组装宏基因组的基因组丰度信息，还可以从 MaxBin 2.0 的结果中识别出哪些微生物在微生物组中占主导地位，以及哪些物种可能共同出现。©2021 威利父子公司。基本方案 1：使用覆盖信息从一个 shotgun 宏基因组中回收基因组基本方案 2：不使用覆盖信息从一个 shotgun 宏基因组中回收基因组基本方案 3：使用每个宏基因组的覆盖信息从多个 shotgun 宏基因组中回收基因组基本方案 4：不使用覆盖信息从多个 shotgun 宏基因组中回收基因组支持方案 1：MaxBin 安装支持方案 2：组装和共组装 NGS 读取。
