Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology.
Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology.
复制标题
病毒组与混合群落宏基因组：方法的选择决定了病毒群落生态学的解释。
DOI：
10.1101/2023.10.15.562385
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Anantharaman,Karthik
中科院分区：
文献类型：
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作者：
Kosmopoulos,JamesC;Klier,KatherineM;Langwig,MargueriteV;Tran,PatriciaQ;Anantharaman,Karthik
背景病毒是地球上最丰富的生物实体之一，其中大多数是未被培养的。从改变微生物生理学到驱动群落动态，病毒是微生物组的基本成员。虽然利用病毒宏基因组学（病毒组学）研究未培养病毒的研究数量正在增加，但缺乏病毒组学研究的标准。病毒组学可以利用来自所有群落成员的总宏基因组（下文称为宏基因组）的病毒的计算发现或使用病毒特异性级分（下文称为病毒组）的物理分离。然而，在恢复和解释从相同的samples.ResultsHere获得的宏基因组和病毒组中的病毒的差异，我们比较了从配对的病毒组和宏基因组中获得的60个不同的样品在人类肠道，土壤，淡水和海洋生态系统的病毒群落。总体而言，从病毒组中获得的病毒群落比从宏基因组中获得的病毒群落具有更大的物种丰富度和总病毒基因组丰度，尽管也有一些例外。尽管如此，宏基因组仍然包含许多病毒基因组中未检测到的病毒基因组。我们还发现在测序时在病毒组与宏基因组中检测到的病毒的预测裂解状态的显著差异。观察到的其他形式的变化包括基因组的存在/不存在，基因组的质量，和编码的蛋白质含量之间的病毒组和宏基因组，但这些差异的大小不同的环境.ConclusionsOverall，我们的研究结果表明，选择的方法可以导致不同的解释病毒群落生态。我们建议，选择是否靶向宏基因组或病毒组研究病毒群落应取决于环境背景和生态问题被问及。然而，我们对研究病毒生态学和进化的研究人员的总体建议是将两种方法结合起来，以最大限度地发挥各自的优势。视频摘要
BackgroundViruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied.ResultsHere, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes had greater species richness and total viral genome abundances than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment.ConclusionsOverall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits.Video Abstract