Recovery of Metagenomic Data from the Aedes aegypti Microbiome using a Reproducible Snakemake Pipeline: MINUUR
Recovery of Metagenomic Data from the Aedes aegypti Microbiome using a Reproducible Snakemake Pipeline: MINUUR
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使用可重复的 Snakemake 管道从埃及伊蚊微生物组中恢复宏基因组数据：MINUUR
DOI：
10.1101/2022.08.09.503283
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发表时间：
2022
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Foo A
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Foo A
正在进行的蚊子微生物群研究旨在发现减少病原体传播的新策略。然而，测序成本，特别是元基因组学，仍然是相当可观的。一个越来越多地被用来洞察宿主相关微生物群的资源是基于蚊子等整个生物体的大量公开可用的基因组数据，其中包括宿主相关微生物的测序读数，并提供了从这些最初以宿主为重点的测序项目中获得额外价值的机会。方法为了分析现有基因组数据中的非宿主读数，我们开发了一个称为MICRUR(使用未映射读数的微生物洞察)的蛇造工作流程。在中非稳定团内部，提取了来自与宿主相关的微生物组的读数，并使用分类分类和元基因组组装进行了特征描述，然后进行了入库和质量评估。我们将这条流水线应用于5个公开可用的埃及伊蚊基因组数据集，包括62个样本和广泛的测序深度。结果我们证明，MARUR恢复了先前识别的门和属，并能够提取与微生物组相关联的细菌元基因组组装基因组(MAG)。在这些MAG中，42个是高质量的代表，>；90%的完整性和<；5%的污染。这些MAG改善了蚊子微生物组的基因组表示，并可用于促进对感兴趣的关键基因的基因组研究。此外，我们发现KRAKEN2分配的读数越多的样本产生的MAG越多。结论我们的元基因组学工作流程，MARUR，被应用于一系列埃及伊蚊基因组样本，以表征微生物组相关的读数。我们确认了与蚊子相关的关键共生体的存在，这些共生体之前已经在其他研究中被发现，并发现了高质量的细菌浆。此外，马里稳定团及其相关文件可在GitHub上免费获得，并为研究人员提供了一个便利的工作流程，以调查任何感兴趣的适用宿主基因组测序数据中包含的微生物组数据。
BackgroundOngoing research of the mosquito microbiome aims to uncover novel strategies to reduce pathogen transmission. Sequencing costs, especially for metagenomics, are however still significant. A resource that is increasingly used to gain insights into host-associated microbiomes is the large amount of publicly available genomic data based on whole organisms like mosquitoes, which includes sequencing reads of the host-associated microbes and provides the opportunity to gain additional value from these initially host-focused sequencing projects.MethodsTo analyse non-host reads from existing genomic data, we developed a snakemake workflow called MINUUR (Microbial INsights Using Unmapped Reads). Within MINUUR, reads derived from the host-associated microbiome were extracted and characterised using taxonomic classifications and metagenome assembly followed by binning and quality assessment. We applied this pipeline to five publicly available Aedes aegypti genomic datasets, consisting of 62 samples with a broad range of sequencing depths.ResultsWe demonstrate that MINUUR recovers previously identified phyla and genera and is able to extract bacterial metagenome assembled genomes (MAGs) associated to the microbiome. Of these MAGS, 42 are high-quality representatives with >90% completeness and <5% contamination. These MAGs improve the genomic representation of the mosquito microbiome and can be used to facilitate genomic investigation of key genes of interest. Furthermore, we show that samples with a high number of KRAKEN2 assigned reads produce more MAGs.ConclusionsOur metagenomics workflow, MINUUR, was applied to a range of Aedes aegypti genomic samples to characterise microbiome-associated reads. We confirm the presence of key mosquito-associated symbionts that have previously been identified in other studies and recovered high-quality bacterial MAGs. In addition, MINUUR and its associated documentation are freely available on GitHub and provide researchers with a convenient workflow to investigate microbiome data included in the sequencing data for any applicable host genome of interest.
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